diff --git a/.gitignore b/.gitignore index 998c701a3d..594ae7f595 100644 --- a/.gitignore +++ b/.gitignore @@ -60,4 +60,4 @@ logger.out* /apps/catalogue/plugins/hl7parser/PropertiesPath.java runmij* modules/compute/protocols/ngsWorkflowRealignmentAndSnpCalling/output/ -modules/compute/demo/ \ No newline at end of file +modules/compute/demo diff --git a/doc/compute/01_compute_introduction.md b/doc/compute/01_compute_introduction.md index a551f8e29d..faebad08db 100644 --- a/doc/compute/01_compute_introduction.md +++ b/doc/compute/01_compute_introduction.md @@ -39,7 +39,7 @@ You can download a ready made binary as follows: >mkdir mycompute >cd mycompute ->wget http://www.molgenis.org/raw-attachment/wiki/ComputeStart/molgenis_compute-dc6ac9c.zip +>wget http://www.molgenis.org/raw-attachment/wiki/ComputeStart/molgenis_compute-fb05467.zip >unzip molgenis_compute-\.zip >mv molgenis_compute-\/* . > @@ -291,7 +291,8 @@ The header of a protocol may contain the following line in which you specify the where `walltime` is the maximum execution time, `mem` is the memory (e.g. 512MB or 4GB), `nodes` is the number of nodes (default=1) and `cores` is the number of cores that you request for the execution of this analysis. ###Get input files -A protocol may be executed in a distributed environment. As a result, the data may not be available on the node where the execution takes place. Therefore, one should first download the data to the execution node. In some distributed environments this may involve a series of statements that one actually does not want to care about. To make this process easier for our users, we come with the following solution. For every file that you want to use in the analysis protocol, you may include the following statement in the protocol before using it. +A protocol may be executed in a distributed environment. As a result, the data may not be available on the node where the execution takes place. Therefore, one should first +the data to the execution node. In some distributed environments this may involve a series of statements that one actually does not want to care about. To make this process easier for our users, we come with the following solution. For every file that you want to use in the analysis protocol, you may include the following statement in the protocol before using it. >getFile "${myInputFile}" diff --git a/modules/compute/demo/debug/output/parameters.csv b/modules/compute/demo/debug/output/parameters.csv deleted file mode 100644 index d5c267d516..0000000000 --- a/modules/compute/demo/debug/output/parameters.csv +++ /dev/null @@ -1,5 +0,0 @@ -Name, defaultValue, description, dataType, hasOne_name -guest, , , , -party, wedding, , , -organizer, , , , -group, , , , organizer \ No newline at end of file diff --git a/modules/compute/demo/debug/output/runlocal.sh b/modules/compute/demo/debug/output/runlocal.sh deleted file mode 100644 index 8ffd1fc1fe..0000000000 --- a/modules/compute/demo/debug/output/runlocal.sh +++ /dev/null @@ -1,32 +0,0 @@ -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -touch $DIR/workflow_csv.started -export PBS_O_WORKDIR=${DIR} -echo Starting with s00_GuestInvitationStep_1... -sh s00_GuestInvitationStep_1.sh -#Dependencies: - -echo Starting with s00_GuestInvitationStep_2... -sh s00_GuestInvitationStep_2.sh -#Dependencies: - -echo Starting with s00_GuestInvitationStep_3... -sh s00_GuestInvitationStep_3.sh -#Dependencies: - -echo Starting with s00_GuestInvitationStep_4... -sh s00_GuestInvitationStep_4.sh -#Dependencies: - -echo Starting with s00_GuestInvitationStep_5... -sh s00_GuestInvitationStep_5.sh -#Dependencies: - -echo Starting with s01_OrganizerInvitationStep_child... -sh s01_OrganizerInvitationStep_child.sh -#Dependencies: - -echo Starting with s01_OrganizerInvitationStep_adult... -sh s01_OrganizerInvitationStep_adult.sh -#Dependencies: - diff --git a/modules/compute/demo/debug/output/s00_GuestInvitationStep_1.sh b/modules/compute/demo/debug/output/s00_GuestInvitationStep_1.sh deleted file mode 100644 index c98dcd058b..0000000000 --- a/modules/compute/demo/debug/output/s00_GuestInvitationStep_1.sh +++ /dev/null @@ -1,5 +0,0 @@ -# Empty header -echo "Hello Charly," -echo "We invite you for our wedding." - -# Empty footer diff --git a/modules/compute/demo/debug/output/s00_GuestInvitationStep_2.sh b/modules/compute/demo/debug/output/s00_GuestInvitationStep_2.sh deleted file mode 100644 index 1026a32010..0000000000 --- a/modules/compute/demo/debug/output/s00_GuestInvitationStep_2.sh +++ /dev/null @@ -1,5 +0,0 @@ -# Empty header -echo "Hello Cindy," -echo "We invite you for our wedding." - -# Empty footer diff --git a/modules/compute/demo/debug/output/s00_GuestInvitationStep_3.sh b/modules/compute/demo/debug/output/s00_GuestInvitationStep_3.sh deleted file mode 100644 index dd88b6d1e6..0000000000 --- a/modules/compute/demo/debug/output/s00_GuestInvitationStep_3.sh +++ /dev/null @@ -1,5 +0,0 @@ -# Empty header -echo "Hello Abel," -echo "We invite you for our wedding." - -# Empty footer diff --git a/modules/compute/demo/debug/output/s00_GuestInvitationStep_4.sh b/modules/compute/demo/debug/output/s00_GuestInvitationStep_4.sh deleted file mode 100644 index 4dbb953394..0000000000 --- a/modules/compute/demo/debug/output/s00_GuestInvitationStep_4.sh +++ /dev/null @@ -1,5 +0,0 @@ -# Empty header -echo "Hello Adam," -echo "We invite you for our wedding." - -# Empty footer diff --git a/modules/compute/demo/debug/output/s00_GuestInvitationStep_5.sh b/modules/compute/demo/debug/output/s00_GuestInvitationStep_5.sh deleted file mode 100644 index 056f2471a1..0000000000 --- a/modules/compute/demo/debug/output/s00_GuestInvitationStep_5.sh +++ /dev/null @@ -1,5 +0,0 @@ -# Empty header -echo "Hello Adri," -echo "We invite you for our wedding." - -# Empty footer diff --git a/modules/compute/demo/debug/output/s01_OrganizerInvitationStep_adult.sh b/modules/compute/demo/debug/output/s01_OrganizerInvitationStep_adult.sh deleted file mode 100644 index 88e768ef0b..0000000000 --- a/modules/compute/demo/debug/output/s01_OrganizerInvitationStep_adult.sh +++ /dev/null @@ -1,11 +0,0 @@ -# Empty header -#FOREACH group - -echo "Dear Otto," -echo "Please organize activities for the adult group." -echo "List of guests:" - echo "Abel" - echo "Adam" - echo "Adri" - -# Empty footer diff --git a/modules/compute/demo/debug/output/s01_OrganizerInvitationStep_child.sh b/modules/compute/demo/debug/output/s01_OrganizerInvitationStep_child.sh deleted file mode 100644 index a9b00445d9..0000000000 --- a/modules/compute/demo/debug/output/s01_OrganizerInvitationStep_child.sh +++ /dev/null @@ -1,10 +0,0 @@ -# Empty header -#FOREACH group - -echo "Dear Oscar," -echo "Please organize activities for the child group." -echo "List of guests:" - echo "Charly" - echo "Cindy" - -# Empty footer diff --git a/modules/compute/demo/debug/output/submit.sh b/modules/compute/demo/debug/output/submit.sh deleted file mode 100644 index 3cd4551870..0000000000 --- a/modules/compute/demo/debug/output/submit.sh +++ /dev/null @@ -1,33 +0,0 @@ -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/workflow_csv.started - -#s00_GuestInvitationStep_1 -s00_GuestInvitationStep_1=$(qsub -N s00_GuestInvitationStep_1 s00_GuestInvitationStep_1.sh) -echo $s00_GuestInvitationStep_1 -sleep 0 -#s00_GuestInvitationStep_2 -s00_GuestInvitationStep_2=$(qsub -N s00_GuestInvitationStep_2 s00_GuestInvitationStep_2.sh) -echo $s00_GuestInvitationStep_2 -sleep 0 -#s00_GuestInvitationStep_3 -s00_GuestInvitationStep_3=$(qsub -N s00_GuestInvitationStep_3 s00_GuestInvitationStep_3.sh) -echo $s00_GuestInvitationStep_3 -sleep 0 -#s00_GuestInvitationStep_4 -s00_GuestInvitationStep_4=$(qsub -N s00_GuestInvitationStep_4 s00_GuestInvitationStep_4.sh) -echo $s00_GuestInvitationStep_4 -sleep 0 -#s00_GuestInvitationStep_5 -s00_GuestInvitationStep_5=$(qsub -N s00_GuestInvitationStep_5 s00_GuestInvitationStep_5.sh) -echo $s00_GuestInvitationStep_5 -sleep 0 -#s01_OrganizerInvitationStep_child -s01_OrganizerInvitationStep_child=$(qsub -N s01_OrganizerInvitationStep_child -W depend=afterok:$s00_GuestInvitationStep_1:$s00_GuestInvitationStep_2 s01_OrganizerInvitationStep_child.sh) -echo $s01_OrganizerInvitationStep_child -sleep 0 -#s01_OrganizerInvitationStep_adult -s01_OrganizerInvitationStep_adult=$(qsub -N s01_OrganizerInvitationStep_adult -W depend=afterok:$s00_GuestInvitationStep_3:$s00_GuestInvitationStep_4:$s00_GuestInvitationStep_5 s01_OrganizerInvitationStep_adult.sh) -echo $s01_OrganizerInvitationStep_adult -sleep 0 - -touch $DIR/workflow_csv.finished \ No newline at end of file diff --git a/modules/compute/demo/debug/output/submitCustom.sh b/modules/compute/demo/debug/output/submitCustom.sh deleted file mode 100644 index d3f728e3cd..0000000000 --- a/modules/compute/demo/debug/output/submitCustom.sh +++ /dev/null @@ -1,31 +0,0 @@ -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/workflow_csv.started - -#s00_GuestInvitationStep_1 -s00_GuestInvitationStep_1=$(qsub -N s00_GuestInvitationStep_1 s00_GuestInvitationStep_1.sh) -echo $s00_GuestInvitationStep_1 -sleep 8 -#s00_GuestInvitationStep_2 -s00_GuestInvitationStep_2=$(qsub -N s00_GuestInvitationStep_2 s00_GuestInvitationStep_2.sh) -echo $s00_GuestInvitationStep_2 -sleep 8 -#s00_GuestInvitationStep_3 -s00_GuestInvitationStep_3=$(qsub -N s00_GuestInvitationStep_3 s00_GuestInvitationStep_3.sh) -echo $s00_GuestInvitationStep_3 -sleep 8 -#s00_GuestInvitationStep_4 -s00_GuestInvitationStep_4=$(qsub -N s00_GuestInvitationStep_4 s00_GuestInvitationStep_4.sh) -echo $s00_GuestInvitationStep_4 -sleep 8 -#s00_GuestInvitationStep_5 -s00_GuestInvitationStep_5=$(qsub -N s00_GuestInvitationStep_5 s00_GuestInvitationStep_5.sh) -echo $s00_GuestInvitationStep_5 -sleep 8 -#s01_OrganizerInvitationStep_child -s01_OrganizerInvitationStep_child=$(qsub -N s01_OrganizerInvitationStep_child -W depend=afterok:$s00_GuestInvitationStep_1:$s00_GuestInvitationStep_2 s01_OrganizerInvitationStep_child.sh) -echo $s01_OrganizerInvitationStep_child -sleep 8 -#s01_OrganizerInvitationStep_adult -s01_OrganizerInvitationStep_adult=$(qsub -N s01_OrganizerInvitationStep_adult -W depend=afterok:$s00_GuestInvitationStep_3:$s00_GuestInvitationStep_4:$s00_GuestInvitationStep_5 s01_OrganizerInvitationStep_adult.sh) -echo $s01_OrganizerInvitationStep_adult -sleep 8 diff --git a/modules/compute/demo/debug/output/workflow.csv b/modules/compute/demo/debug/output/workflow.csv deleted file mode 100644 index ae737660f7..0000000000 --- a/modules/compute/demo/debug/output/workflow.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -GuestInvitationStep, GuestInvitation, -OrganizerInvitationStep, OrganizerInvitation, GuestInvitationStep \ No newline at end of file diff --git a/modules/compute/demo/debug/output/worksheet.csv b/modules/compute/demo/debug/output/worksheet.csv deleted file mode 100644 index 41d68adaea..0000000000 --- a/modules/compute/demo/debug/output/worksheet.csv +++ /dev/null @@ -1,6 +0,0 @@ -guest, group, organizer -Charly, child, Oscar -Cindy, child, Oscar -Abel, adult, Otto -Adam, adult, Otto -Adri, adult, Otto \ No newline at end of file diff --git a/modules/compute/demo/debug/parameters.csv b/modules/compute/demo/debug/parameters.csv deleted file mode 100644 index d5c267d516..0000000000 --- a/modules/compute/demo/debug/parameters.csv +++ /dev/null @@ -1,5 +0,0 @@ -Name, defaultValue, description, dataType, hasOne_name -guest, , , , -party, wedding, , , -organizer, , , , -group, , , , organizer \ No newline at end of file diff --git a/modules/compute/demo/debug/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/debug/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/debug/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/debug/protocols/Footer.ftl b/modules/compute/demo/debug/protocols/Footer.ftl deleted file mode 100644 index 7e17f56898..0000000000 --- a/modules/compute/demo/debug/protocols/Footer.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty footer \ No newline at end of file diff --git a/modules/compute/demo/debug/protocols/GuestInvitation.ftl b/modules/compute/demo/debug/protocols/GuestInvitation.ftl deleted file mode 100644 index 4d55adf9f6..0000000000 --- a/modules/compute/demo/debug/protocols/GuestInvitation.ftl +++ /dev/null @@ -1,2 +0,0 @@ -echo "Hello ${guest}," -echo "We invite you for our ${party}." \ No newline at end of file diff --git a/modules/compute/demo/debug/protocols/Header.ftl b/modules/compute/demo/debug/protocols/Header.ftl deleted file mode 100644 index 0d9b0b2514..0000000000 --- a/modules/compute/demo/debug/protocols/Header.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty header diff --git a/modules/compute/demo/debug/protocols/OrganizerInvitation.ftl b/modules/compute/demo/debug/protocols/OrganizerInvitation.ftl deleted file mode 100644 index 2c66a46a18..0000000000 --- a/modules/compute/demo/debug/protocols/OrganizerInvitation.ftl +++ /dev/null @@ -1,8 +0,0 @@ -#FOREACH group - -echo "Dear ${organizer}," -echo "Please organize activities for the ${group} group." -echo "List of guests:" -<#list guest as g> - echo "${g}" - \ No newline at end of file diff --git a/modules/compute/demo/debug/workflow.csv b/modules/compute/demo/debug/workflow.csv deleted file mode 100644 index ae737660f7..0000000000 --- a/modules/compute/demo/debug/workflow.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -GuestInvitationStep, GuestInvitation, -OrganizerInvitationStep, OrganizerInvitation, GuestInvitationStep \ No newline at end of file diff --git a/modules/compute/demo/debug/worksheet.csv b/modules/compute/demo/debug/worksheet.csv deleted file mode 100644 index 41d68adaea..0000000000 --- a/modules/compute/demo/debug/worksheet.csv +++ /dev/null @@ -1,6 +0,0 @@ -guest, group, organizer -Charly, child, Oscar -Cindy, child, Oscar -Abel, adult, Otto -Adam, adult, Otto -Adri, adult, Otto \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/parameters.csv b/modules/compute/demo/debugFolding/inputdir/parameters.csv deleted file mode 100644 index 82d8dd3e75..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/parameters.csv +++ /dev/null @@ -1,287 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,gaf,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -defaultInterpreter,#!/bin/bash,,, -library,${fileprefix},,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -workflowHeader,NGSHeader.ftl,,, -tooldir,${root}/tools,root dir for tools,string, -gafhome,/target/gpfs2/gaf,gaf home dir,string, -gaftools,${gafhome}/tools,,string, -gafscripts,${gaftools}/scripts,,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -transferDataScript,${scriptdir}/transferData.sh,,, -demultiplexscript,${gafscripts}/demultiplex.R,,string, -demultiplexWorkflowFile,${McDir}/workflows/in-house_workflow_demultiplex.csv,,string, -workflowFile,${McDir}/workflows/in-house_workflow_realignmentAndSnpCalling.csv,,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -intervallistdir,${resdir}/${genome}/intervals,,, -capturingKit,,,, -baitintervals,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileIDtest}.interval_list,,, -targetintervals,${intervallistdir}/${capturingKit}_exons_${genome}_${indexfileIDtest}.interval_list,,, -baitsbed,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileIDtest}.bed,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -datadir,${root}/groups/in-house,root dir for data,string, -allRawNgsDataDir,${datadir}/rawdata/ngs/,"Contains all rawdata (i.e., *.fq files)",string, -allRunDemultiplexDir,${datadir}/runs/,Demultiplex historical data specific runs directory,string, -runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell},,string, -runJobsDir,${allRunDemultiplexDir}/${runPrefix}/jobs/,Run specific job scripts directory,string, -runResultsDir,${allRunDemultiplexDir}/${runPrefix}/results/,Store demultiplexed results here,string, -rawdatadir,${allRawNgsDataDir}/${runPrefix},"contains rawdata (i.e., *.fq files)",string, -arraydir,${datadir}/rawdata/array,,, -fileprefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane},first part of file name,string, -srinputfile,${rawdatadir}/${fileprefix}.fq.gz,use for single read,, -leftinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_1.fq.gz,use as hack to simulate paired end data,, -rightinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_2.fq.gz,use as hack to simulate paired end data,, -leftinputfile,${rawdatadir}/${fileprefix}_1.fq.gz,fastq file with left read of sequence,string, -rightinputfile,${rawdatadir}/${fileprefix}_2.fq.gz,fastq file with right read of sequence,string, -projectdir,${datadir}/projects/${project}/${McId},project folder for this insilico run,, -runtimelog,${projectdir}/${fileprefix}.runtime.log,,, -projectrawdatadir,${projectdir}/rawdata/ngs/,project specific rawdata directory for (demultiplexed) reads,string, -projectrawarraydatadir,${projectdir}/rawdata/array/,"Contains project specific rawdata (i.e., Genome Studio files)",string, -intermediatedir,${tempprojectdir}/${project}/${McId}/,store intermediate results here; empty at end of project,, -projectJobsDir,${projectdir}/jobs/,Project specific job scripts directory,string, -projectLogsDir,${projectdir}/logs/,Project specific log directory,string, -projectResultsDir,${projectdir}/results/,Store final results here; a sub set of the primary outputs that we want to keep/archive are moved to this dir; afterwards the remaining files from the intermediate dir will be lost when we clean up.,string, -contact,,,, -project,,,,"contact,allRawNgsDataDir" -sequencingStartDate,,,, -sequencer,,,, -run,,,,"sequencer,sequencingStartDate,runJobsDir,runResultsDir" -flowcell,,,,"run,runJobsDir,runResultsDir" -seqType,,,, -lane,,,,"flowcell,seqType" -barcode,,,, -leftbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_1,use these in case of demultiplexed files,, -rightbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_2,idem,, -leftbarcodefq,${leftbarcode}.fq,,, -rightbarcodefq,${rightbarcode}.fq,,, -outputleftright,"${leftbarcodefq},${rightbarcodefq}","file locations for both ends where we save demultiplexed reads, given respecive project folder and barcode",string, -srbarcodefq,${projectrawdatadir}/${fileprefix}_${barcode}.fq,,, -demultiplexinfodir,${datadir}/demultiplexinfo,directory in which we store logs and discarded reads files,string, -logfile,${demultiplexinfodir}/${fileprefix}.log.txt,log file with statistics on demultiplexing process,string, -runtimelogdemultiplex,${demultiplexinfodir}/${fileprefix}.runtime.log,,, -discardleft,${demultiplexinfodir}/${fileprefix}_DISCARD_1.fq,file that contains 'left ends' of sequences with undected barcodes,string, -discardright,${demultiplexinfodir}/${fileprefix}_DISCARD_2.fq,file that contains 'right ends' of sequences with undected barcodes,string, -leftbarcodefqgz,${leftbarcodefq}.gz,"gziped file, in project raw data dir",, -rightbarcodefqgz,${rightbarcodefq}.gz,,, -srbarcodefqgz,${srbarcodefq}.gz,,, -leftfile,${intermediatedir}/${fileprefix}_${barcode}_1,,, -rightfile,${intermediatedir}/${fileprefix}_${barcode}_2,,, -leftfastqczip,${leftfile}.fq_fastqc.zip,(fastqc.ftl),, -rightfastqczip,${rightfile}.fq_fastqc.zip,(fastqc.ftl),, -leftfastqcsummarytxt,${leftfile}_fastqcsummary.txt,(fastqc.ftl),, -rightfastqcsummarytxt,${rightfile}_fastqcsummary.txt,(fastqc.ftl),, -leftfastqcsummarylog,${leftfile}_fastqcsummary.log,(fastqc.ftl),, -rightfastqcsummarylog,${rightfile}_fastqcsummary.log,(fastqc.ftl),, -fastqcjar,${tooldir}/fastqc-v0.7.0/fastqc,(fastqc.ftl),, -leftbwaout,${leftfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -rightbwaout,${rightfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -bwaalignjar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_align),, -bwaaligncores,4,(bwa_align),, -fileWithIndexID,${intermediatedir}/${fileprefix}_${barcode}.${indexfileID},Just a shorthand in this parameters file,, -samfile,${fileWithIndexID}.sam,(bwa_sampe),, -bwasampejar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_sampe),, -bamfile,${fileWithIndexID}.bam,(sam to bam),, -picard,${tooldir}/picard-tools-1.61,,, -samtobamjar,${picard}/SamFormatConverter.jar,,, -sortedbam,${fileWithIndexID}.sorted.bam,,, -sortedbamindex,${fileWithIndexID}.sorted.bam.bai,,, -sortsamjar,${picard}/SortSam.jar,,, -buildbamindexjar,${picard}/BuildBamIndex.jar,,, -alignmentmetricsjar,${picard}/CollectAlignmentSummaryMetrics.jar,,, -alignmentmetrics,${fileWithIndexID}.alignmentmetrics,,, -gcbiasmetricsjar,${picard}/CollectGcBiasMetrics.jar,,, -gcbiasmetrics,${fileWithIndexID}.gcbiasmetrics,,, -gcbiasmetricspdf,${gcbiasmetrics}.pdf,,, -insertsizemetricsjar,${picard}/CollectInsertSizeMetrics.jar,,, -insertsizemetrics,${fileWithIndexID}.insertsizemetrics,,, -insertsizemetricspdf,${insertsizemetrics}.pdf,,, -recreateinsertsizepdfR,${tooldir}/createInsertSizePlot/createInsertSizePlot.R,Recreate the insert size pdf's with R,, -meanqualitybycyclejar,${picard}/MeanQualityByCycle.jar,,, -meanqualitybycycle,${fileWithIndexID}.meanqualitybycycle,,, -meanqualitybycyclepdf,${fileWithIndexID}.meanqualitybycycle.pdf,,, -qualityscoredistributionjar,${picard}/QualityScoreDistribution.jar,,, -qualityscoredistribution,${fileWithIndexID}.qualityscoredistribution,,, -qualityscoredistributionpdf,${fileWithIndexID}.qualityscoredistribution.pdf,,, -hsmetricsjar,${picard}/CalculateHsMetrics.jar,,, -hsmetrics,${fileWithIndexID}.hsmetrics,,, -bamindexstatsjar,${picard}/BamIndexStats.jar,,, -bamindexstats,${fileWithIndexID}.bamindexstats,(picardQC),, -dedupbam,${fileWithIndexID}.dedup.bam,,, -dedupbamindex,${fileWithIndexID}.dedup.bam.bai,,, -dedupmetrics,${fileWithIndexID}.dedup.metrics,,, -markduplicatesjar,${picard}/MarkDuplicates.jar,,, -dbsnprod,${resdir}/${genome}/dbsnp/dbsnp_129_b37_${indexfileID}.rod,,, -pilot1KgVcf,${resdir}/${genome}/indels/1kg_pilot_release_merged_indels_sites_${genome}_${indexfileID}.vcf,,, -realignTargets,${fileWithIndexID}.realign.target.intervals,,, -genomeAnalysisTKjar,${tooldir}/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar,,, -genomeAnalysisTKjar1411,${tooldir}/GATK-1.4-11-g845c0b1/dist/GenomeAnalysisTK.jar,,, -realignedbam,${fileWithIndexID}.realigned.bam,,, -matefixedbam,${fileWithIndexID}.matefixed.bam,,, -matefixedbamindex,${matefixedbam}.bai,,, -matefixedcovariatecsv,${fileWithIndexID}.matefixed.covariates.table.csv,,, -fixmateinformationjar,${picard}/FixMateInformation.jar,,, -recalbam,${fileWithIndexID}.recal.bam,(samsortrecal),, -sortedrecalbam,${fileWithIndexID}.recal.sorted.bam,(samsortrecal),, -sortedrecalbamindex,${sortedrecalbam}.bai,(samsortrecal),, -mergesamfilesjar,${picard}/MergeSamFiles.jar,(MergeBam),, -externalSampleID,,(MergeBam),,"project,capturingKit,arrayFile,arrayID,seqType" -mergedbam,${intermediatedir}/${externalSampleID}.${indexfileID}.merged.bam,(MergeBam),,externalSampleID -mergedbamindex,${mergedbam}.bai,(MergeBam),,mergedbam -sortedrecalcovariatecsv,${fileWithIndexID}.recal.covariate.table.csv,,, -recalstatsbeforedir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.before,,, -recalstatsafterdir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.after,,, -cyclecovariatebefore,${recalstatsbeforedir}/${lane}.CycleCovariate.dat,,, -cyclecovariateafter,${recalstatsafterdir}/${lane}.CycleCovariate.dat,,, -analyzecovariatesjar,${tooldir}/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar,,, -sample,${intermediatedir}/${externalSampleID},(PicardQCRecal),, -samplealignmentmetrics,${sample}.alignmentmetrics,(PicardQCRecal),, -samplegcbiasmetrics,${sample}.gcbiasmetrics,(PicardQCRecal),, -samplegcbiasmetricspdf,${samplegcbiasmetrics}.pdf,(PicardQCRecal),, -sampleinsertsizemetrics,${sample}.insertsizemetrics,(PicardQCRecal),, -sampleinsertsizemetricspdf,${sampleinsertsizemetrics}.pdf,(PicardQCRecal),, -samplemeanqualitybycycle,${sample}.meanqualitybycycle,(PicardQCRecal),, -samplemeanqualitybycyclepdf,${samplemeanqualitybycycle}.pdf,(PicardQCRecal),, -samplequalityscoredistribution,${sample}.qualityscoredistribution,(PicardQCRecal),, -samplequalityscoredistributionpdf,${samplequalityscoredistribution}.pdf,(PicardQCRecal),, -samplebamindexstats,${sample}.bamindexstats.pdf,(PicardQCRecal),, -samplehsmetrics,${sample}.hsmetrics,(PicardQCRecal),, -coveragescript,${scriptdir}/coverage.R,(Coverage),, -samplecoverageplotpdf,${sample}.coverageplot.pdf,(Coverage),, -coveragegatk,${sample}.coveragegatk,(CoverageGATK),, -cumcoveragescriptgatk,${tooldir}/scripts/plot_cumulative_coverage-1.1.R,(CoverageGATK),, -indelsbed,${sample}.indels.bed,,, -indelsvcf,${sample}.indels.vcf,,, -indelsverboseoutput,${sample}.indels.verboseoutput.txt,,, -filterSingleSampleCallsperl,${tooldir}/scripts/filterSingleSampleCalls.pl,,, -indelsfilteredbed,${sample}.indels.filtered.bed,,, -makeIndelMaskpyton,${tooldir}/scripts/makeIndelMask.py,,, -indelsmaskbed,${sample}.indels.mask.bed,(MakeIndelsMask),, -snpsvcf,${sample}.snps.vcf,,, -snpsvariantannotatedvcf,${sample}.snps.variant.annotated.vcf,,, -annotationPath,${resdir}/${genome}/dbsnp,,, -dbsnpSNPstxt,${annotationPath}/dbSNP135.tabdelim.table,(GenomicAnnotator),, -snpsgenomicannotatedvcf,${sample}.snps.genomic.annotated.vcf,(GenomicAnnotator),, -dbsnpvcf,${annotationPath}/dbsnp_135.b37.vcf,(VariantAnnotator),, -dbsnpexsitesafter129vcf,${annotationPath}/dbsnp_135.b37.excluding_sites_after_129.vcf,(ConcordanceCheck),, -snpeffjar,${tooldir}/snpEff_2_0_5/snpEff.jar,(VariantAnnotator),, -snpeffconfig,${tooldir}/snpEff_2_0_5/snpEff.config,(VariantAnnotator),, -snpeffsummaryhtml,${sample}.snps.final.snpEff_summary.html,(VariantAnnotator),, -snpeffintermediate,${sample}.snps.intermediate.snpEff.vcf,(VariantAnnotator),, -snpsfinal,${sample}.snps.final,(VariantAnnotator),, -snpsfinalvcf,${snpsfinal}.vcf,(VariantAnnotator),, -snpsgenomicannotatedfilteredvcf,${sample}.snps.variant.genomic.annotated.filtered.vcf,(VariantFiltration),, -vcf2tablepy,${tooldir}/GATK-1.0.5069/Sting/python/vcf2table.py,(VcfToTable),, -snpsfinalvcftable,${snpsfinalvcf}.table,(VcfToTable),, -snpannotationstatspl,${tooldir}/scripts/snp_annotation_stats.pl,(VcfToTable),, -createsnptablescriptpath,${tooldir}/scripts/createSNPTable_19mar2012,,, -createsnptablescript,${createsnptablescriptpath}/createSNPTable.R,,, -snpsfinalvcftabletype,${snpsfinal}.type.txt,(VcfToTable),, -snpsfinalvcftableclass,${snpsfinal}.class.txt,(VcfToTable),, -snpsfinalvcftableimpact,${snpsfinal}.impact.txt,(VcfToTable),, -snpstatsprefix,${intermediatedir}/${project}.snps.final,,, -typetableout,${snpstatsprefix}.type.tex,QCReport,, -classtableout,${snpstatsprefix}.class.tex,QCReport,, -impacttableout,${snpstatsprefix}.impact.tex,QCReport,, -arrayFile,,,, -arrayID,,,, -finalreport,${arraydir}/${externalSampleID}_FinalReport.txt,(ConcordanceCheck),, -finalreporttmpdir,${intermediatedir}/${externalSampleID}_FinalReport.txt,(ConcordanceCheck),, -familylist,${sample}.familylist.txt,(ConcordanceCheck),, -arraytmpmap,${sample}.concordance.tmp.map,(ConcordanceCheck),, -arraymapfile,${sample}.concordance.map,(ConcordanceCheck),, -sampleconcordancefile,${sample}.concordance.ngsVSarray.txt,(ConcordanceCheck),, -getstatisticsscriptpath,${tooldir}/getStatistics_23jan2012,QCStatistics,, -getStatisticsScript,${getstatisticsscriptpath}/getStatistics.R,QCStatistics,, -qcstatisticscolnames,${getstatisticsscriptpath}/NiceColumnNames.csv,QCStatistics,, -gaffig,${getstatisticsscriptpath}/GAFpipeline.png,QCStatistics,, -gccfig,${getstatisticsscriptpath}/Agilent_experiment.png,QCStatistics,, -qcdir,${projectdir}/qc,QCStatistics,, -qcbaitset,${qcdir}/projectbaitset.txt,QCStatistics,, -qcdedupmetricsout,${qcdir}/dedupmetrics.txt,QCStatistics,, -qcstatisticscsv,${qcdir}/${project}_QCStatistics.csv,QCStatistics,, -qcstatisticstex,${qcdir}/${project}_qcstatisticstable.tex,QCStatistics,, -qcstatisticsdescription,${qcdir}/${project}_qcstatisticsdescription.tex,QCStatistics,, -qcstatisticstexreport,${qcdir}/${project}_QCReport.tex,QCStatistics,, -demultiplexstats,${qcdir}/${fileprefix}.log.txt,QCStatistics,, -dot,${tooldir}/graphviz-2.28.0/bin/dot,QCStatistics,, -workflowpng,${qcdir}/${project}_workflow.png,QCStatistics,, -getDedupInfoScript,${scriptdir}/getDedupInfo_23mar2012/getDedupInfo.R,,, -#,,,, -filenamePartSeperator,_,,, -filenamePrefix,${sequencingStartDate}${filenamePartSeperator}${sequencer}${filenamePartSeperator}${run}${filenamePartSeperator}${flowcell}${filenamePartSeperator}L${lane},,string, -fastqExtension,.fq,,string, -gzipExtension,.gz,,string, -md5sumExtension,.md5,,string, -#,,,, -filenameSuffixPE1,1,,, -filenameSuffixPE2,2,,, -filenameSuffixDiscardedReads,DISCARDED,,, -#,,,, -fastqFilenameSR,${filenamePrefix}${fastqExtension},,, -fastqFilenameNoBarcodeSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},,, -fastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -fastqFilenameNoBarcodePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenameNoBarcodePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -#,,,, -fastqChecksumFilenameSR,${fastqFilenameSR}${md5sumExtension},,, -fastqChecksumFilenameNoBarcodeSR,${fastqFilenameNoBarcodeSR}${md5sumExtension},,, -fastqChecksumFilenamePE1,${fastqFilenamePE1}${md5sumExtension},,, -fastqChecksumFilenamePE2,${fastqFilenamePE2}${md5sumExtension},,, -fastqChecksumFilenameNoBarcodePE1,${fastqFilenameNoBarcodePE1}${md5sumExtension},,, -fastqChecksumFilenameNoBarcodePE2,${fastqFilenameNoBarcodePE2}${md5sumExtension},,, -#,,,, -compressedFastqFilenameSR,${fastqFilenameSR}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenameNoBarcodeSR,${fastqFilenameNoBarcodeSR}${gzipExtension},,string, -compressedFastqFilenamePE1,${fastqFilenamePE1}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE2,${fastqFilenamePE2}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenameNoBarcodePE1,${fastqFilenameNoBarcodePE1}${gzipExtension},,, -compressedFastqFilenameNoBarcodePE2,${fastqFilenameNoBarcodePE2}${gzipExtension},,, -#,,,, -demultiplexedSampleFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilenameSR,${demultiplexedSampleFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilepathSR,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR},,, -compressedDemultiplexedSampleFastqFilepathPE1,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1},,, -compressedDemultiplexedSampleFastqFilepathPE2,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2},,, -#,,,, -demultiplexedSampleFastqChecksumFilenameSR,${demultiplexedSampleFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -log,log.log,,, -# -fastqcVersion,v0.7.0,,, -bwaVersion,0.5.8c_patched,,, -picardVersion,1.61,,, \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/AnalyzeCovariates.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/AnalyzeCovariates.ftl deleted file mode 100644 index b5e242a610..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/AnalyzeCovariates.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:45:00 - -inputs "${matefixedcovariatecsv}" -inputs "${sortedrecalcovariatecsv}" -alloutputsexist \ -"${cyclecovariatebefore}" \ -"${cyclecovariateafter}" - -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -java -jar -Xmx4g ${analyzecovariatesjar} -l INFO \ --resources ${indexfile} \ ---recal_file ${matefixedcovariatecsv} \ --outputDir ${recalstatsbeforedir} \ --Rscript ${rscript} \ --ignoreQ 5 - -java -jar -Xmx4g ${analyzecovariatesjar} -l INFO \ --resources ${indexfile} \ ---recal_file ${sortedrecalcovariatecsv} \ --outputDir ${recalstatsafterdir} \ --Rscript ${rscript} \ --ignoreQ 5 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/BwaAlignLeft.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/BwaAlignLeft.ftl deleted file mode 100644 index d94ed62fca..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/BwaAlignLeft.ftl +++ /dev/null @@ -1,29 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=15:00:00 nodes=1 cores=4 mem=6 -#TARGETS - -module load bwa/${bwaVersion} - -getFile ${indexfile} -getFile ${leftbarcodefqgz} -alloutputsexist "${leftbwaout}" - -mkdir -p "${intermediatedir}" - -bwa aln \ -${indexfile} \ -${leftbarcodefqgz} \ --t ${bwaaligncores} \ --f ${leftbwaout} - - -putFile ${leftbwaout} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/BwaAlignRight.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/BwaAlignRight.ftl deleted file mode 100644 index 5e3c800dae..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/BwaAlignRight.ftl +++ /dev/null @@ -1,31 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -<#if seqType == "PE"> -#MOLGENIS walltime=15:00:00 nodes=1 cores=4 mem=6 -#TARGETS - -module load bwa/${bwaVersion} - -getFile ${indexfile} -getFile ${rightbarcodefqgz} -alloutputsexist "${rightbwaout}" - -mkdir -p "${intermediatedir}" - -bwa aln \ -${indexfile} \ -${rightbarcodefqgz} \ --t ${bwaaligncores} \ --f ${rightbwaout} - -putFile ${rightbwaout} - - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/BwaSampe.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/BwaSampe.ftl deleted file mode 100644 index a9e25248f3..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/BwaSampe.ftl +++ /dev/null @@ -1,35 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=23:59:00 -#TARGETS - -module load bwa/${bwaVersion} - -getFile ${indexfile} -getFile ${leftbwaout} -getFile ${rightbwaout} -getFile ${leftbarcodefqgz} -getFile ${rightbarcodefqgz} -alloutputsexist "${samfile}" - -<#if seqType == "PE">bwa sampe -P \<#else>bwa samse \ --p illumina \ --i ${lane} \ --m ${externalSampleID} \ --l ${library} \ -${indexfile} \ -${leftbwaout} \ -<#if seqType == "PE">${rightbwaout} \ -${leftbarcodefqgz} \ -<#if seqType == "PE">${rightbarcodefqgz} \ --f ${samfile} - -putFile ${samfile} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CheckRawdataPresence.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CheckRawdataPresence.ftl deleted file mode 100644 index caa1c94708..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CheckRawdataPresence.ftl +++ /dev/null @@ -1,90 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=1:00:00 nodes=1 cores=1 mem=1 -#FOREACH flowcell, lane, seqType, filenamePrefix - -# -# For each lane. -# -<#if seqType == "SR"> - - # - # Check the complete lane files. - # - ls ${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenameSR} - ls ${allRawNgsDataDir}/${runPrefix}/${fastqChecksumFilenameSR} - - <#if barcode[0] == "None"> - <#else> - # - # Check demultiplexing success. - # - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.read_count_check.passed - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.log - - # - # For the demultiplexed sample FastQ files: - # - <#list demultiplexedSampleFastqFilenameSR as fileToCheck> - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedSampleFastqFilenameSR[fileToCheck_index]} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]} - - - # - # Same for the discarded reads FastQ file. - # - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedDiscardedFastqChecksumFilenameSR} - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedDiscardedFastqFilenameSR} - - - -<#elseif seqType == "PE"> - - # - # Check the complete lane files. - # - ls ${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenamePE1} - ls ${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenamePE2} - ls ${allRawNgsDataDir}/${runPrefix}/${fastqChecksumFilenamePE1} - ls ${allRawNgsDataDir}/${runPrefix}/${fastqChecksumFilenamePE2} - - <#if barcode[0] == "None"> - <#else> - # - # Check demultiplexing success. - # - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.read_count_check.passed - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.log - - # - # For the demultiplexed sample FastQ files: - # - <#list demultiplexedSampleFastqFilenamePE1 as fileToCheck> - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedSampleFastqFilenamePE1[fileToCheck_index]} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]} - - <#list demultiplexedSampleFastqFilenamePE2 as fileToCheck> - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedSampleFastqFilenamePE2[fileToCheck_index]} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]} - - - # - # Same for the discarded reads FastQ file. - # - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedDiscardedFastqFilenamePE1} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedDiscardedFastqChecksumFilenamePE1} - - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedDiscardedFastqFilenamePE2} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedDiscardedFastqChecksumFilenamePE2} - - - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/ConcordanceCheck.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/ConcordanceCheck.ftl deleted file mode 100644 index f4fc9bf6c2..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/ConcordanceCheck.ftl +++ /dev/null @@ -1,363 +0,0 @@ -# -# ===================================================== -# $Id: ConcordanceCheck.ftl 12159 2012-06-13 10:56:41Z freerkvandijk $ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/ConcordanceCheck.ftl $ -# $LastChangedDate: 2012-06-13 12:56:41 +0200 (Wed, 13 Jun 2012) $ -# $LastChangedRevision: 12159 $ -# $LastChangedBy: freerkvandijk $ -# ===================================================== -# - -#MOLGENIS walltime=09:59:00 mem=4 -#FOREACH externalSampleID - -inputs "${mergedbam}" -alloutputsexist \ -"${finalreport}" \ -"${familylist}" \ -"${sample}.concordance.fam" \ -"${sample}.concordance.lgen" \ -"${arraytmpmap}" \ -"${arraymapfile}" \ -"${sample}.ped" \ -"${sample}.genotypeArray.vcf" \ -"${sample}.genotypeArray.bed" \ -"${sample}.genotypeArray.fasta" \ -"${sample}.genotypeArray.aligned_to_ref.vcf.out" \ -"${sample}.genotypeArray.aligned_to_ref.vcf" \ -"${sample}.genotypeArray.aligned_to_ref.lifted_over.vcf" \ -"${sample}.genotypeArray.header.txt" \ -"${sample}.genotypeArray.headerless.vcf" \ -"${sample}.genotypeArray.updated.header.vcf" \ -"${sample}.concordance.allSites.vcf" \ -"${sample}.genotypeArray.updated.header.interval_list" \ -"${sample}.concordance.q20.dp10.vcf" \ -"${sample}.concordance.q20.dp10.eval" \ -"${sampleconcordancefile}" - -if test ! -e ${finalreport}; -then - echo "name, step, nSNPs, PercDbSNP, Ti/Tv_known, Ti/Tv_Novel, All_comp_het_called_het, Known_comp_het_called_het, Non-Ref_Sensitivity, Non-Ref_discrepancy, Overall_concordance" > ${sampleconcordancefile} - echo "[1] NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA" >> ${sampleconcordancefile} -else - #Check finalreport on "missing" alleles. Also, see if we can fix missing alleles somewhere in GenomeStudio - awk '{ if ($3 != "-" || $4 != "-") print $0};' ${finalreport} \ - > ${sample}_FinalReport.txt.tmp - - ##Set R library path - export PATH=${R_HOME}/bin:<#noparse>${PATH} - export R_LIBS=${R_LIBS} - - ##Push sample belonging to family "1" into list.txt - echo '1 ${externalSampleID}' > ${familylist} - - ######################################################################### - ######################################################################### - ######################################################################### - # Use 'probe positions' to check whether the array file / final report is in build 36 or build 37. - # In some cases the the position is erroneously one too small. In those cases, we add one to all positions in the array file / final report. - - # Load ten rs-ids and positions of ten probes that should be present on build 36 and also on build 37. - # The difference in positions between none of the probes on b36 and b37 is 1. - # Therefore, we can safely test whether a position matches on position n or n+1... - - rs[0]=rs4830576 - b36[0]=8245875 - b37[0]=8285875 - rs[1]=rs922257 - b36[1]=20391000 - b37[1]=20481079 - rs[2]=rs2168861 - b36[2]=31773234 - b37[2]=31863313 - rs[3]=rs5918076 - b36[3]=40718890 - b37[3]=40833946 - rs[4]=rs5936538 - b36[4]=69241401 - b37[4]=69324676 - rs[5]=rs4826938 - b36[5]=105496014 - b37[5]=105609358 - rs[6]=rs2208263 - b36[6]=115330016 - b37[6]=115415988 - rs[7]=rs1279816 - b36[7]=123183295 - b37[7]=123355614 - rs[8]=rs370713 - b36[8]=138470059 - b37[8]=138642393 - rs[9]=rs2266828 - b36[9]=149374751 - b37[9]=149624093 - - # Find out which build was used. This info is stored in $build (build36, build37, N/A, ERROR) - build="N/A" - - # Find out whether we have to increase all positions in the array file with 1. - # Store this in the variable $increase1 ("true", "false") - increase1="false" - - i=0 - unset ready - while [ -z $ready ] - do - position=`awk '$1 == "'<#noparse>${rs[$i]}'" {print $7}' ${sample}_FinalReport.txt.tmp` - - echo "<#noparse>${rs[$i]} has position <#noparse>${position}" - - # does the probe exist in this file? - if [ ! -z $position ] - then - ready="ready" - - if [ <#noparse>${position//$'\r'} == ${b36[$i]} ] - then - # we are on build 36 - build="build36" - elif [ <#noparse>${position//$'\r'} == ${b37[$i]} ] - then - # we are on build 37 - build="build37" - elif [ <#noparse>$((${position//$'\r'} + 1)) == ${b36[$i]} ] - then - # we are on build 36 (after increasing position with 1) - build="build36" - increase1="true" - elif [ <#noparse>$((${position//$'\r'} + 1)) == ${b37[$i]} ] - then - # we are on build 37 (after increasing position with 1) - build="build37" - increase1="true" - else - # we are neither on build 36 nor on build 37, according to this test - build="ERROR" - fi - fi - - # stop if we have tested all probes - if [ <#noparse>${#rs[@]} -le $(($i+1)) ] - then - ready="ready" - fi - - # increase counter - i=$[$i+1] - done - - # Now copy the array file / final report to the tmp dir - # Or, if increase1 == "true" then use awk to add one to the positions and redirect standard out to tmp dir - - if [ $increase1 == "false" ] - then - cp ${sample}_FinalReport.txt.tmp ${finalreporttmpdir} - elif [ $increase1 == "true" ] - then - awk '{$7=$7+1; print $1,$2,$3,$4,$5,$6,$7}' OFS="\t" ${sample}_FinalReport.txt.tmp > ${finalreporttmpdir} - else - echo "ERROR, variable increase1 should be either false or true" - fi - - - ######################################################################### - ######################################################################### - ######################################################################### - - ##Create .fam, .lgen and .map file from sample_report.txt - sed -e '1,10d' ${finalreporttmpdir} | awk '{print "1",$2,"0","0","0","1"}' | uniq > ${sample}.concordance.fam - sed -e '1,10d' ${finalreporttmpdir} | awk '{print "1",$2,$1,$3,$4}' | awk -f ${tooldir}/scripts/RecodeFRToZero.awk > ${sample}.concordance.lgen - sed -e '1,10d' ${finalreporttmpdir} | awk '{print $6,$1,"0",$7}' OFS="\t" | sort -k1n -k4n | uniq > ${arraytmpmap} - grep -P '^[123456789]' ${arraytmpmap} | sort -k1n -k4n > ${arraymapfile} - grep -P '^[X]\s' ${arraytmpmap} | sort -k4n >> ${arraymapfile} - grep -P '^[Y]\s' ${arraytmpmap} | sort -k4n >> ${arraymapfile} - - #?# MD vraagt: wat doen --lfile en --out, en horen die gelijk te zijn? - ##Create .bed and other files (keep sample from sample_list.txt). - ${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink \ - --lfile ${sample}.concordance \ - --recode \ - --out ${sample}.concordance \ - --keep ${familylist} - - ##Create genotype VCF for sample - ${tooldir}/plink-1.08/plink108 \ - --recode-vcf \ - --ped ${sample}.concordance.ped \ - --map ${arraymapfile} \ - --out ${sample}.concordance - - ##Rename plink.vcf to sample.vcf - mv ${sample}.concordance.vcf ${sample}.genotypeArray.vcf - - ##Replace chr23 and 24 with X and Y - perl -pi -e 's/^23/X/' ${sample}.genotypeArray.vcf - perl -pi -e 's/^24/Y/' ${sample}.genotypeArray.vcf - - ##Remove family ID from sample in header genotype VCF - perl -pi -e 's/1_${externalSampleID}/${externalSampleID}/' ${sample}.genotypeArray.vcf - - ##Create binary ped (.bed) and make tab-delimited .fasta file for all genotypes - sed -e 's/chr//' ${sample}.genotypeArray.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2}}' \ - > ${sample}.genotypeArray.bed - - ${tooldir}/BEDTools-Version-2.11.2/bin/fastaFromBed \ - -fi ${resdir}/b36/hs_ref_b36.fasta \ - -bed ${sample}.genotypeArray.bed \ - -fo ${sample}.genotypeArray.fasta -tab - - - #################################### - if [ $build == "build36" ] - then # File is on build36 - - ##Align vcf to reference AND DO NOT FLIP STRANDS!!! (genotype data is already in forward-forward format) If flipping is needed use "-f" command before sample.genotype_array.vcf - perl ${tooldir}/scripts/align-vcf-to-ref.pl \ - ${sample}.genotypeArray.vcf \ - ${sample}.genotypeArray.fasta \ - ${sample}.genotypeArray.aligned_to_ref.vcf \ - > ${sample}.genotypeArray.aligned_to_ref.vcf.out - - ##Lift over sample.genotype_array.aligned_to_ref.vcf from build 36 to build 37 - perl ${tooldir}/GATK-1.0.5069/Sting/perl/liftOverVCF.pl \ - -vcf ${sample}.genotypeArray.aligned_to_ref.vcf \ - -gatk ${tooldir}/GATK-1.0.5069/Sting \ - -chain ${resdir}/b36/chainfiles/b36ToHg19.broad.over.chain \ - -newRef ${resdir}/hg19/indices/human_g1k_v37 \ - -oldRef ${resdir}/b36/hs_ref_b36 \ - -tmp ${tempdir} \ - -out ${sample}.genotypeArray.aligned_to_ref.lifted_over.vcf - - ##Some GATK versions sort header alphabetically, which results in wrong individual genotypes. So cut header from "original" sample.genotype_array.vcf and replace in sample.genotype_array.aligned_to_ref.lifted_over.out - head -3 ${sample}.genotypeArray.vcf > ${sample}.genotypeArray.header.txt - - sed '1,4d' ${sample}.genotypeArray.aligned_to_ref.lifted_over.vcf \ - > ${sample}.genotypeArray.headerless.vcf - - cat ${sample}.genotypeArray.header.txt \ - ${sample}.genotypeArray.headerless.vcf \ - > ${sample}.genotypeArray.updated.header.vcf - - ##Create interval_list of CHIP SNPs to call SNPs in sequence data on - perl ${tooldir}/scripts/iChip_pos_to_interval_list.pl \ - ${sample}.genotypeArray.updated.header.vcf \ - ${sample}.genotypeArray.updated.header.interval_list - - ###THESE STEPS USE NEWER VERSION OF GATK THAN OTHER STEPS IN ANALYSIS PIPELINE!!! - ##Call SNPs on all positions known to be on array and output VCF (including hom ref calls) - java -Xmx4g -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -l INFO \ - -T UnifiedGenotyper \ - -R ${indexfile} \ - -I ${mergedbam} \ - -o ${sample}.concordance.allSites.vcf \ - -stand_call_conf 30.0 \ - -stand_emit_conf 10.0 \ - -out_mode EMIT_ALL_SITES \ - -L ${sample}.genotypeArray.updated.header.interval_list - - ##Change FILTER column from GATK "called SNPs". All SNPs having Q20 & DP10 change to "PASS", all other SNPs are "filtered" (not used in concordance check) - perl ${tooldir}/scripts/change_vcf_filter.pl \ - ${sample}.concordance.allSites.vcf \ - ${sample}.concordance.q20.dp10.vcf 10 20 - - ##Calculate condordance between genotype SNPs and GATK "called SNPs" - java -Xmx2g -Djava.io.tmpdir=${tempdir} -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -T VariantEval \ - -eval:eval,VCF ${sample}.concordance.q20.dp10.vcf \ - -comp:comp_immuno,VCF ${sample}.genotypeArray.updated.header.vcf \ - -o ${sample}.concordance.q20.dp10.eval \ - -R ${indexfile} \ - -D:dbSNP,VCF ${dbsnpexsitesafter129vcf} \ - -EV GenotypeConcordance - - ##Create concordance output file with header - echo 'name, step, nSNPs, PercDbSNP, Ti/Tv_known, Ti/Tv_Novel, All_comp_het_called_het, Known_comp_het_called_het, Non-Ref_Sensitivity, Non-Ref_discrepancy, Overall_concordance' \ - > ${sampleconcordancefile} - - ##Retrieve name,step,#SNPs,%dbSNP,Ti/Tv known,Ti/Tv Novel,Non-Ref Sensitivity,Non-Ref discrepancy,Overall concordance from sample.q20_dp10_concordance.eval - ##Don't forget to add .libPaths("/target/gpfs2/gcc/tools/GATK-1.3-24-gc8b1c92/public/R") to your ~/.Rprofile - Rscript ${tooldir}/scripts/extract_info_GATK_variantEval_V3.R \ - --in ${sample}.concordance.q20.dp10.eval \ - --step q20_dp10_concordance \ - --name ${externalSampleID} \ - --comp comp_immuno \ - --header >> ${sampleconcordancefile} - fi - if [ $build == "build37" ] - then - ################################### - #Arrayfile is on build 37 - - ##Align vcf to reference AND DO NOT FLIP STRANDS!!! (genotype data is already in forward-forward format) If flipping is needed use "-f" command before sample.genotype_array.vcf - perl ${tooldir}/scripts/align-vcf-to-ref.pl \ - ${sample}.genotypeArray.vcf \ - ${sample}.genotypeArray.fasta \ - ${sample}.genotypeArray.aligned_to_ref.vcf \ - > ${sample}.genotypeArray.aligned_to_ref.vcf.out - - ##Some GATK versions sort header alphabetically, which results in wrong individual genotypes. So cut header from "original" sample.genotype_array.vcf and replace in sample.genotype_array.aligned_to_ref.lifted_over.out - head -3 ${sample}.genotypeArray.vcf > ${sample}.genotypeArray.header.txt - - sed '1,3d' ${sample}.genotypeArray.aligned_to_ref.vcf \ - > ${sample}.genotypeArray.headerless.vcf - - cat ${sample}.genotypeArray.header.txt \ - ${sample}.genotypeArray.headerless.vcf \ - > ${sample}.genotypeArray.updated.header.vcf - - ##Create interval_list of CHIP SNPs to call SNPs in sequence data on - perl ${tooldir}/scripts/iChip_pos_to_interval_list.pl \ - ${sample}.genotypeArray.updated.header.vcf \ - ${sample}.genotypeArray.updated.header.interval_list - - ###THESE STEPS USE NEWER VERSION OF GATK THAN OTHER STEPS IN ANALYSIS PIPELINE!!! - ##Call SNPs on all positions known to be on array and output VCF (including hom ref calls) - java -Xmx4g -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -l INFO \ - -T UnifiedGenotyper \ - -R ${indexfile} \ - -I ${mergedbam} \ - -o ${sample}.concordance.allSites.vcf \ - -stand_call_conf 30.0 \ - -stand_emit_conf 10.0 \ - -out_mode EMIT_ALL_SITES \ - -L ${sample}.genotypeArray.updated.header.interval_list - - ##Change FILTER column from GATK "called SNPs". All SNPs having Q20 & DP10 change to "PASS", all other SNPs are "filtered" (not used in concordance check) - perl ${tooldir}/scripts/change_vcf_filter.pl \ - ${sample}.concordance.allSites.vcf \ - ${sample}.concordance.q20.dp10.vcf 10 20 - - ##Calculate condordance between genotype SNPs and GATK "called SNPs" - java -Xmx2g -Djava.io.tmpdir=${tempdir} -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -T VariantEval \ - -eval:eval,VCF ${sample}.concordance.q20.dp10.vcf \ - -comp:comp_immuno,VCF ${sample}.genotypeArray.updated.header.vcf \ - -o ${sample}.concordance.q20.dp10.eval \ - -R ${indexfile} \ - -D:dbSNP,VCF ${dbsnpexsitesafter129vcf} \ - -EV GenotypeConcordance - - ##Create concordance output file with header - echo 'name, step, nSNPs, PercDbSNP, Ti/Tv_known, Ti/Tv_Novel, All_comp_het_called_het, Known_comp_het_called_het, Non-Ref_Sensitivity, Non-Ref_discrepancy, Overall_concordance' \ - > ${sampleconcordancefile} - - ##Retrieve name,step,#SNPs,%dbSNP,Ti/Tv known,Ti/Tv Novel,Non-Ref Sensitivity,Non-Ref discrepancy,Overall concordance from sample.q20_dp10_concordance.eval - ##Don't forget to add .libPaths("/target/gpfs2/gcc/tools/GATK-1.3-24-gc8b1c92/public/R") to your ~/.Rprofile - Rscript ${tooldir}/scripts/extract_info_GATK_variantEval_V3.R \ - --in ${sample}.concordance.q20.dp10.eval \ - --step q20_dp10_concordance \ - --name ${externalSampleID} \ - --comp comp_immuno \ - --header >> ${sampleconcordancefile} - fi - if [ $build == "N/A" ] - then - echo "ERROR: unsure which build was used. None of the probes we checked was found in the array file." - fi - if [ $build == "ERROR" ] - then - echo "ERROR: one of the probe in the array file has an unexpected position. Therefore, we are not able to tell which build was used." - fi -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CopyFqToRawdatadir.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CopyFqToRawdatadir.ftl deleted file mode 100644 index a8380f147e..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CopyFqToRawdatadir.ftl +++ /dev/null @@ -1,22 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. ${root}/gcc.bashrc - -umask 0007 - -${gafscripts}/copy_fq_to_rawdatadir.pl \ --rawdatadir ${runResultsDir} \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CopyFqToResultsDirREADMEtemplate.tex b/modules/compute/demo/debugFolding/inputdir/protocols/CopyFqToResultsDirREADMEtemplate.tex deleted file mode 100644 index 3434a8a345..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CopyFqToResultsDirREADMEtemplate.tex +++ /dev/null @@ -1,90 +0,0 @@ -\documentclass[a4paper,12pt]{article} -\usepackage{nameref} -\usepackage{grffile} -\usepackage{graphicx} -\usepackage[strings]{underscore} -\usepackage{verbatim} -\usepackage{wrapfig} -\usepackage{lastpage} - -\begin{comment} -# -# ===================================================== -# $Id: QCReportTemplate.tex 11716 2012-04-20 11:55:31Z mdijkstra $ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/QCReportTemplate.tex $ -# $LastChangedDate: 2012-04-20 13:55:31 +0200 (Fri, 20 Apr 2012) $ -# $LastChangedRevision: 11716 $ -# $LastChangedBy: mdijkstra $ -# ===================================================== -# -\end{comment} - -\newenvironment{narrow}[2]{ - \begin{list}{}{ - \setlength{\leftmargin}{#1} - \setlength{\rightmargin}{#2} - \setlength{\listparindent}{\parindent} - \setlength{\itemindent}{\parindent} - \setlength{\parsep}{\parskip} - } - \item[] -}{\end{list}} - - -\begin{document} -\thispagestyle{empty} -\vspace{40mm} - - -\clearpage -\section*{README} - -This zip file contains the following files and directories: -\subsection*{SNPs} -*.snps.final.vcf = All SNP calls in VCF format. (eg. to be used for Cartagenia etc.) - -\noindent*.snps.final.vcf.table = All SNP calls in tab-delimited format. - -\subsection*{QC} -*_fastqc.zip = Information about the quality of the raw sequence reads. Please read the FastQC manual page for detailed information. - -\#\#\#OPTIONAL\#\#\# - -\noindent*.genotypeArray.updated.header.vcf = Sample genotype calls in VCF format. - - -\subsection*{QC/statistics} -*metric files = Metrics used to compile the QC report. For information/documentation about all metrics not explained in the QC report we refer to the Picard documentation. - - -\subsection*{} - - -${project}.csv = This file contains all the information for the project. If samples were pooled information about the used barcodes etc. can be found here. - -\noindent ${project}_QCReport.pdf = QC report containing all important QC metrics per sample. - - -\subsection*{} - - -\subsection*{Additional files} - -*.merged.bam = The BAM file containing all (un)aligned reads after removing duplicates and quality score recalibration. -This is the final alignment on which SNP calling was executed. - -\noindent*.merged.bam.bai = The index file of the *.merged.bam. - -\noindent*.fq.gz = gzipped FASTQ file containing all reads, if multiple samples were pooled these files contain the demultiplexed reads per flowcell, lane, barcode combination. The exact combination for each sample can be found in the ${project}.csv file. - -\noindent*.fq.md5 = the md5sum for the corresponding FASTQ file. - - -\subsection*{} - - -\section*{Documentation} -FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ -Picard: http://picard.sourceforge.net/picard-metric-definitions.shtml - -\end{document} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CopyToResultsDir.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CopyToResultsDir.ftl deleted file mode 100644 index 42d0b3a8b9..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CopyToResultsDir.ftl +++ /dev/null @@ -1,124 +0,0 @@ -# -# ===================================================== -# $Id: CopyToResultsDir.ftl 12202 2012-06-15 09:10:27Z freerkvandijk $ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/CopyToResultsDir.ftl $ -# $LastChangedDate: 2012-06-15 11:10:27 +0200 (Fri, 15 Jun 2012) $ -# $LastChangedRevision: 12202 $ -# $LastChangedBy: freerkvandijk $ -# ===================================================== -# - -#MOLGENIS walltime=23:59:00 -#FOREACH project - - -alloutputsexist "${projectResultsDir}/${project}.zip" - -# Change permissions - -umask 0007 - - -# Make result directories -mkdir -p ${projectResultsDir}/rawdata -mkdir -p ${projectResultsDir}/alignment -mkdir -p ${projectResultsDir}/coverage -mkdir -p ${projectResultsDir}/snps -mkdir -p ${projectResultsDir}/qc/statistics - - -# Copy error, out and finished logs to project jobs directory - -cp ${projectJobsDir}/*.out ${projectLogsDir} -cp ${projectJobsDir}/*.err ${projectLogsDir} -cp ${projectJobsDir}/*.log ${projectLogsDir} - -# Copy project csv file to project results directory - -cp ${projectJobsDir}/${project}.csv ${projectResultsDir} - - -# Create symlinks for all fastq and md5 files to the project results directory - -cp -rs ${projectrawdatadir} ${projectResultsDir}/rawdata - - -# Copy fastQC output to results directory -cp ${intermediatedir}/*_fastqc.zip ${projectResultsDir}/qc - - -# Copy dedup metrics to results directory -cp ${intermediatedir}/*.dedup.metrics ${projectResultsDir}/qc/statistics - - -# Create md5 sum and copy merged BAM plus index plus md5 sum to results directory -<#if 0 < mergedbam?size> - <#list 0..(mergedbam?size-1) as index> - md5sum ${mergedbam[index]} > ${mergedbam[index]}.md5 - md5sum ${mergedbamindex[index]} > ${mergedbamindex[index]}.md5 - cp ${mergedbam[index]}* ${projectResultsDir}/alignment - - - -# Copy alignment stats (lane and sample) to results directory - -cp ${intermediatedir}/*.alignmentmetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.gcbiasmetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.insertsizemetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.meanqualitybycycle ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.qualityscoredistribution ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.hsmetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.bamindexstats ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.pdf ${projectResultsDir}/qc/statistics - - -# Copy coverage stats (for future reference) to results directory - -cp ${intermediatedir}/*.coverage* ${projectResultsDir}/coverage - - -# Copy final vcf and vcf.table to results directory - -<#list sample as s> - - cp ${s}.snps.final.vcf ${projectResultsDir}/snps - cp ${s}.snps.final.vcf.table ${projectResultsDir}/snps - - - # Copy genotype array vcf to results directory - - if [ -f "${s}.genotypeArray.updated.header.vcf" ] - then - cp ${s}.genotypeArray.updated.header.vcf ${projectResultsDir}/qc - fi - - cp ${s}.concordance.ngsVSarray.txt ${projectResultsDir}/qc - - - -# Copy QC report to results directory - -cp ${qcdir}/${project}_QCReport.pdf ${projectResultsDir} - - -# save latex README template in file -echo "<#include "CopyToResultsDirREADMEtemplate.tex"/>" > ${projectResultsDir}/README.txt - -pdflatex -output-directory=${projectResultsDir} ${projectResultsDir}/README.txt - - -# Create zip file for all "small text" files - -cd ${projectResultsDir} - -zip -r ${projectResultsDir}/${project}.zip snps -zip -gr ${projectResultsDir}/${project}.zip qc -zip -g ${projectResultsDir}/${project}.zip ${project}.csv -zip -g ${projectResultsDir}/${project}.zip README.pdf -zip -g ${projectResultsDir}/${project}.zip ${project}_QCReport.pdf - -# Create md5sum for zip file - -cd ${projectResultsDir} - -md5sum ${project}.zip > ${projectResultsDir}/${project}.zip.md5 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CopyToResultsDirREADMEtemplate.tex b/modules/compute/demo/debugFolding/inputdir/protocols/CopyToResultsDirREADMEtemplate.tex deleted file mode 100644 index 9c3af69aeb..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CopyToResultsDirREADMEtemplate.tex +++ /dev/null @@ -1,90 +0,0 @@ -\documentclass[a4paper,12pt]{article} -\usepackage{nameref} -\usepackage{grffile} -\usepackage{graphicx} -\usepackage[strings]{underscore} -\usepackage{verbatim} -\usepackage{wrapfig} -\usepackage{lastpage} - -\begin{comment} -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# -\end{comment} - -\newenvironment{narrow}[2]{ - \begin{list}{}{ - \setlength{\leftmargin}{#1} - \setlength{\rightmargin}{#2} - \setlength{\listparindent}{\parindent} - \setlength{\itemindent}{\parindent} - \setlength{\parsep}{\parskip} - } - \item[] -}{\end{list}} - - -\begin{document} -\thispagestyle{empty} -\vspace{40mm} - - -\clearpage -\section*{README} - -This zip file contains the following files and directories: -\subsection*{SNPs} -*.snps.final.vcf = All SNP calls in VCF format. (eg. to be used for Cartagenia etc.) - -\noindent*.snps.final.vcf.table = All SNP calls in tab-delimited format. - -\subsection*{QC} -*_fastqc.zip = Information about the quality of the raw sequence reads. Please read the FastQC manual page for detailed information. - -\#\#\#OPTIONAL\#\#\# - -\noindent*.genotypeArray.updated.header.vcf = Sample genotype calls in VCF format. - - -\subsection*{QC/statistics} -*metric files = Metrics used to compile the QC report. For information/documentation about all metrics not explained in the QC report we refer to the Picard documentation. - - -\subsection*{} - - -${project}.csv = This file contains all the information for the project. If samples were pooled information about the used barcodes etc. can be found here. - -\noindent ${project}_QCReport.pdf = QC report containing all important QC metrics per sample. - - -\subsection*{} - - -\subsection*{Additional files} - -*.merged.bam = The BAM file containing all (un)aligned reads after removing duplicates and quality score recalibration. -This is the final alignment on which SNP calling was executed. - -\noindent*.merged.bam.bai = The index file of the *.merged.bam. - -\noindent*.fq.gz = gzipped FASTQ file containing all reads, if multiple samples were pooled these files contain the demultiplexed reads per flowcell, lane, barcode combination. The exact combination for each sample can be found in the ${project}.csv file. - -\noindent*.fq.md5 = the md5sum for the corresponding FASTQ file. - - -\subsection*{} - - -\section*{Documentation} -FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ -Picard: http://picard.sourceforge.net/picard-metric-definitions.shtml - -\end{document} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Covariates.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Covariates.ftl deleted file mode 100644 index 3ec1209a94..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Covariates.ftl +++ /dev/null @@ -1,27 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -inputs "${matefixedbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -alloutputsexist "${matefixedcovariatecsv}" - -java -jar -Xmx4g \ -${genomeAnalysisTKjar} -l INFO \ --T CountCovariates \ --U ALLOW_UNINDEXED_BAM \ --R ${indexfile} \ ---DBSNP ${dbsnprod} \ --I ${matefixedbam} \ --cov ReadGroupcovariate \ --cov QualityScoreCovariate \ --cov CycleCovariate \ --cov DinucCovariate \ --recalFile ${matefixedcovariatecsv} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CovariatesAfter.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CovariatesAfter.ftl deleted file mode 100644 index cf4d8616c2..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CovariatesAfter.ftl +++ /dev/null @@ -1,11 +0,0 @@ -#MOLGENIS walltime=66:00:00 - -###### Renaming because we call another protocol: - -#input: -<#assign matefixedbam=sortedrecalbam /> - -#output: -<#assign matefixedcovariatecsv=sortedrecalcovariatecsv /> - -<#include "Covariates.ftl" /> diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CovariatesBefore.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CovariatesBefore.ftl deleted file mode 100644 index 3bdc72cadc..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CovariatesBefore.ftl +++ /dev/null @@ -1,3 +0,0 @@ -#MOLGENIS walltime=66:00:00 - -<#include "Covariates.ftl" /> diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Coverage.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Coverage.ftl deleted file mode 100644 index 9fc45a6bf3..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Coverage.ftl +++ /dev/null @@ -1,28 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=65:59:00 mem=12 cores=1 -#FOREACH externalSampleID - -inputs "${mergedbam}" -alloutputsexist "${sample}.coverage.csv" \ -"${samplecoverageplotpdf}" \ -"${sample}.coverage.Rdata" - -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -Rscript ${coveragescript} \ ---bam ${mergedbam} \ ---chromosome 1 \ ---interval_list ${targetintervals} \ ---csv ${sample}.coverage.csv \ ---pdf ${samplecoverageplotpdf} \ ---Rcovlist ${sample}.coverage.Rdata diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CoverageGATK.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CoverageGATK.ftl deleted file mode 100644 index 34480bfdaf..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CoverageGATK.ftl +++ /dev/null @@ -1,43 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=66:00:00 nodes=1 cores=1 mem=12 -#FOREACH externalSampleID - -inputs "${mergedbam}" "${mergedbamindex}" "${indexfile}" -<#if capturingKit != "None">inputs "${targetintervals}" -alloutputsexist "${coveragegatk}" \ -"${coveragegatk}.sample_cumulative_coverage_counts" \ -"${coveragegatk}.sample_cumulative_coverage_proportions" \ -"${coveragegatk}.sample_interval_statistics" \ -"${coveragegatk}.sample_interval_summary" \ -"${coveragegatk}.sample_statistics" \ -"${coveragegatk}.sample_summary" \ -"${coveragegatk}.cumulative_coverage.pdf" - -export PATH=${JAVA_HOME}/bin:<#noparse>${PATH} -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -java -Djava.io.tmpdir=${tempdir} -Xmx12g -jar \ -${genomeAnalysisTKjar} \ --T DepthOfCoverage \ --R ${indexfile} \ --I ${mergedbam} \ --o ${coveragegatk} \ --ct 1 -ct 2 -ct 5 -ct 10 -ct 15 -ct 20 -ct 30 -ct 40 -ct 50<#if capturingKit != "None"> \ --L ${targetintervals} - -#Create coverage graphs for sample -${rscript} ${cumcoveragescriptgatk} \ ---in ${coveragegatk}.sample_cumulative_coverage_proportions \ ---out ${coveragegatk}.cumulative_coverage.pdf \ ---max-depth 100 \ ---title "Cumulative coverage ${externalSampleID}" diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CreateFinalReport.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CreateFinalReport.ftl deleted file mode 100644 index 1601b0fa90..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CreateFinalReport.ftl +++ /dev/null @@ -1,25 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/Recalibrate.ftl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: mdijkstra $ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. ${root}/gcc.bashrc - -umask 0007 - - - -perl ${scriptdir}/create_per_sample_finalreport.pl \ --inputdir ${arraydir} \ --outputdir ${arraydir} \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CreateInhouseProjects.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CreateInhouseProjects.ftl deleted file mode 100644 index 1ab780929c..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CreateInhouseProjects.ftl +++ /dev/null @@ -1,91 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:10:00 -#FOREACH project - -# -# Change permissions. -# -umask 0007 - -# -# Create project dirs. -# -mkdir -p ${projectrawarraydatadir} -mkdir -p ${projectrawdatadir} -mkdir -p ${projectJobsDir} -mkdir -p ${projectLogsDir} -mkdir -p ${intermediatedir} -mkdir -p ${projectResultsDir} -mkdir -p ${qcdir} - -# -# Create symlinks to the raw data required to analyse this project -# -# For each sequence file (could be multiple per sample): -# -<#list internalSampleID as sample> - - <#if seqType[sample_index] == "SR"> - - <#if barcode[sample_index] == "None"> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenameSR[sample_index]} ${projectrawdatadir}/${compressedFastqFilenameNoBarcodeSR[sample_index]} - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${fastqChecksumFilenameSR[sample_index]} ${projectrawdatadir}/${fastqChecksumFilenameNoBarcodeSR[sample_index]} - - # Also add a symlink for the alignment step: - # ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenamePE1[sample_index]} ${projectrawdatadir}/${compressedFastqFilenameNoBarcodePE1[sample_index]} - <#else> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedDemultiplexedSampleFastqFilenameSR[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${demultiplexedSampleFastqChecksumFilenameSR} ${projectrawdatadir}/ - - - <#elseif seqType[sample_index] == "PE"> - - <#if barcode[sample_index] == "None"> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenamePE1[sample_index]} ${projectrawdatadir}/${compressedFastqFilenameNoBarcodePE1[sample_index]} - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenamePE2[sample_index]} ${projectrawdatadir}/${compressedFastqFilenameNoBarcodePE2[sample_index]} - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${fastqChecksumFilenamePE1[sample_index]} ${projectrawdatadir}/${fastqChecksumFilenameNoBarcodePE1[sample_index]} - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${fastqChecksumFilenamePE2[sample_index]} ${projectrawdatadir}/${fastqChecksumFilenameNoBarcodePE2[sample_index]} - <#else> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedDemultiplexedSampleFastqFilenamePE1[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedDemultiplexedSampleFastqFilenamePE2[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${demultiplexedSampleFastqChecksumFilenamePE1[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${demultiplexedSampleFastqChecksumFilenamePE2[sample_index]} ${projectrawdatadir}/ - - - - - - -# -# TODO: array for each sample: -# - -# -# Create subset of samples for this project. -# -<#--<#assign unfolded = unfoldParametersCSV(parameters) /> -<#list unfolded as sampleSequenceDetails> -echo ${sampleSequenceDetails} >> ${projectJobsDir}/${project}.csv ---> -${scriptdir}/extract_samples_from_GAF_list.pl --i ${McWorksheet} --o ${projectJobsDir}/${project}.csv --c project --q ${project} - -# -# Execute MOLGENIS/compute to create job scripts to analyse this project. -# -sh ${McDir}/molgenis_compute.sh \ --worksheet=${projectJobsDir}/${project}.csv \ --parameters=${McParameters} \ --workflow=${workflowFile} \ --protocols=${McProtocols}/ \ --templates=${McTemplates}/ \ --scripts=${projectJobsDir}/ \ --id=${McId} diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/CreateInhouseRuns.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/CreateInhouseRuns.ftl deleted file mode 100644 index 692e85fc62..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/CreateInhouseRuns.ftl +++ /dev/null @@ -1,44 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:10:00 -#FOREACH run, flowcell - -# -# Change permissions. -# -umask 0007 - -# -# Create run dirs. -# -mkdir -p ${runJobsDir} -mkdir -p ${runResultsDir} - -# -# Create subset of samples for this project. -# -<#--<#assign unfolded = unfoldParametersCSV(parameters) /> -<#list unfolded as sampleSequenceDetails> -echo ${sampleSequenceDetails} >> ${runJobsDir}/${run}.csv ---> -${scriptdir}/extract_samples_from_GAF_list.pl --i ${McWorksheet} --o ${runJobsDir}/${run}.csv --c run --q ${run} - -# -# Execute MOLGENIS/compute to create job scripts to analyse this project. -# -sh ${McDir}/molgenis_compute.sh \ --worksheet=${runJobsDir}/${run}.csv \ --parameters=${McParameters} \ --workflow=${demultiplexWorkflowFile} \ --protocols=${McProtocols}/ \ --templates=${McTemplates}/ \ --scripts=${runJobsDir}/ \ --id=${McId} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Demultiplex.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Demultiplex.ftl deleted file mode 100644 index 47db2715de..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Demultiplex.ftl +++ /dev/null @@ -1,277 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate 20120807$ -# $LastChangedRevision$ -# $LastChangedBy WBKoetsier$ -# ===================================================== -# - -#MOLGENIS walltime=48:00:00 nodes=1 cores=4 mem=1 -#FOREACH flowcell, lane, seqType, filenamePrefix - -export PATH=${R_HOME}/bin:<#noparse>${PATH} - -# -# Check if we need to run this step or wether demultiplexing was already executed successfully in a previous run. -# -# Note: we don't check for presence of the actual demultiplexed reads, but for empty file indicating successfull demultipxing instead -# where success is based on a comparison of the amount of reads in the multiplexed input file and the total amount of reads in -# the demultiplexed output files: these counts should be the same. -# -alloutputsexist "${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.passed" - -# -# For each lane demultiplex rawdata. -# -<#if seqType == "SR"> - - <#if barcode[0] == "None"> - # - # Do nothing. - # - touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.skipped - <#elseif barcodeType[0] == "RPI"> - # - # Do nothing. - # - touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.skipped - <#elseif barcodeType[0] == "GAF"> - # - # Check if the files required for demultiplexing are present. - # - inputs "${runResultsDir}/${compressedFastqFilenameSR}" - - # - # Read count of the input file. - # Note: we actually count lines, which equals reads * 4 for FastQ files. - # - reads_in_1=$(gzip -cd ${runResultsDir}/${compressedFastqFilenameSR} | wc -l) - - # - # Demultiplex the multiplexed, gzipped FastQ file. - # - Rscript ${demultiplexscript} --bcs '${csv(barcode)}' \ - --mpr1 ${runResultsDir}/${compressedFastqFilenameSR} \ - --dmr1 '${csv(compressedDemultiplexedSampleFastqFilepathSR)}' \ - --ukr1 ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenameSR} \ - --tm MP \ - > ${runResultsDir}/${filenamePrefix}.demultiplex.log - - # - # Read count of the output file. - # - summed_reads_out_1=0 - - # - # For the demultiplexed, uncompressed FastQ files: - # 1. Calculate MD5Sums. - # 2. Count the amount of lines(, which equals to reads * 4) per file. - # 3. Update the sum of lines of all files. - # - <#list demultiplexedSampleFastqFilenameSR as fileToCheck> - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe - md5sum <${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe | \ - sed 's/ -/ ${fileToCheck}/' > ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR[fileToCheck_index]} | \ - tee ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - - - # - # Same for the discarded, uncompressed FastQ file. - # - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe - md5sum <${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe | \ - sed 's/ -/ ${demultiplexedDiscardedFastqFilenameSR}/' > ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenameSR} | \ - tee ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - # - # Flush disk caches to disk to make sure we don't loose any demultiplexed data - # when a machine crashes and some of the "written" data was in a write buffer. - # - sync - - # - # Read count sanity check. - # - if (( $reads_in_1 == $summed_reads_out_1 )) - then touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.passed - else touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.FAILED - fi - - <#else> - # - # Found unknown barcode type! - # - echo "FATAL: unknown barcode type found for ${filenamePrefix}" - exit 1 - - -<#elseif seqType == "PE"> - - <#if barcode[0] == "None"> - # - # Do nothing. - # - touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.skipped - <#elseif barcodeType[0] == "RPI"> - # - # Illumina demultiplexed files: do not demultiplex, but do perform a read count check between reads 1 and 2 - # - # Check if the files required for the read count check are present. - # - <#list compressedDemultiplexedSampleFastqFilenamePE1 as fileToCheck> - inputs "${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1[fileToCheck_index]}" - - - <#list compressedDemultiplexedSampleFastqFilenamePE2 as fileToCheck> - inputs "${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2[fileToCheck_index]}" - - - # - # Read count of the input file. - # Note: we actually count lines, which equals reads * 4 for FastQ files. - # Read count sanity check for the inputs. - # For PE data the amount of reads in both input files must be the same! - # - <#list compressedDemultiplexedSampleFastqFilenamePE1 as fileToCheck> - reads_1=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1[fileToCheck_index]} | wc -l) - reads_2=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2[fileToCheck_index]} | wc -l) - if (( $reads_1 != $reads_2)) - then touch ${runResultsDir}/${filenamePrefix}_${barcode[fileToCheck_index]}.read_count_check.FAILED - echo "FATAL: Number of reads in both ${filenamePrefix}_${barcode[fileToCheck_index]} FastQ files not the same!" - exit 1 - fi - - - <#elseif barcodeType[0] == "GAF"> - # - # Check if the files required for demultiplexing are present. - # - inputs "${runResultsDir}/${compressedFastqFilenamePE1}" - inputs "${runResultsDir}/${compressedFastqFilenamePE2}" - - # - # Read count of the input file. - # Note: we actually count lines, which equals reads * 4 for FastQ files. - # - reads_in_1=$(gzip -cd ${runResultsDir}/${compressedFastqFilenamePE1} | wc -l) - reads_in_2=$(gzip -cd ${runResultsDir}/${compressedFastqFilenamePE2} | wc -l) - - # - # Read count sanity check for the inputs. - # For PE data the amount of reads in both input files must be the same! - # - if (( $reads_in_1 != $reads_in_2)) - then touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.FAILED - echo "FATAL: cannot demultiplex ${filenamePrefix}. Number of reads in both specified PE FastQ input files not the same!" - exit 1 - fi - - # - # Demultiplex the multiplexed, gzipped FastQ file. - # - Rscript ${demultiplexscript} --bcs '${csv(barcode)}' \ - --mpr1 ${runResultsDir}/${compressedFastqFilenamePE1} \ - --mpr2 ${runResultsDir}/${compressedFastqFilenamePE2} \ - --dmr1 '${csv(compressedDemultiplexedSampleFastqFilepathPE1)}' \ - --dmr2 '${csv(compressedDemultiplexedSampleFastqFilepathPE2)}' \ - --ukr1 ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE1} \ - --ukr2 ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE2} \ - --tm MP \ - > ${runResultsDir}/${filenamePrefix}.demultiplex.log - - # - # Read count of the output file. - # - summed_reads_out_1=0 - summed_reads_out_2=0 - - # - # For the demultiplexed, uncompressed FastQ files: - # 1. Calculate MD5Sums. - # 2. Count the amount of lines(, which equals to reads * 4) per file. - # 3. Update the sum of lines of all files. - # - <#list demultiplexedSampleFastqFilenamePE1 as fileToCheck> - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe - md5sum <${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe | \ - sed 's/ -/ ${fileToCheck}/' > ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1[fileToCheck_index]} | \ - tee ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - - <#list demultiplexedSampleFastqFilenamePE2 as fileToCheck> - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe - md5sum <${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe | \ - sed 's/ -/ ${fileToCheck}/' > ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2[fileToCheck_index]} | \ - tee ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe - summed_reads_out_2=$(( $summed_reads_out_2 + $this_read_count )) - - - # - # Same for the discarded, uncompressed FastQ files. - # - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe - md5sum <${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe | \ - sed 's/ -/ ${demultiplexedDiscardedFastqFilenamePE1}/' > ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE1} | \ - tee ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe - md5sum <${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe | \ - sed 's/ -/ ${demultiplexedDiscardedFastqFilenamePE2}/' > ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE2} | \ - tee ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe - summed_reads_out_2=$(( $summed_reads_out_2 + $this_read_count )) - - # - # Flush disk caches to disk to make sure we don't loose any demultiplexed data - # when a machine crashes and some of the "written" data was in a write buffer. - # - sync - - # - # Read count sanity check. - # - if (( $reads_in_1 == $summed_reads_out_1 )) && (( $reads_in_2 == $summed_reads_out_2)) - then touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.passed - else touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.FAILED - fi - - <#else> - # - # Found unknown barcode type! - # - echo "FATAL: unknown barcode type found for ${filenamePrefix}" - exit 1 - - - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Fastqc.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Fastqc.ftl deleted file mode 100644 index ee27ccd9f1..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Fastqc.ftl +++ /dev/null @@ -1,62 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=08:00:00 nodes=1 cores=1 mem=1 -#TARGETS - -module load fastqc/${fastqcVersion} - -<#if seqType == "SR"> - getFile ${srbarcodefqgz} - alloutputsexist \ - "${leftfastqczip}" \ - "${leftfastqcsummarytxt}" \ - "${leftfastqcsummarylog}" \ -<#else> - getFile "${leftbarcodefqgz}" - getFile "${rightbarcodefqgz}" - alloutputsexist \ - "${leftfastqczip}" \ - "${leftfastqcsummarytxt}" \ - "${leftfastqcsummarylog}" \ - "${rightfastqczip}" \ - "${rightfastqcsummarytxt}" \ - "${rightfastqcsummarylog}" - - -# first make logdir... -mkdir -p "${intermediatedir}" - -# pair1 -fastqc ${leftbarcodefqgz} \ --Djava.io.tmpdir=${tempdir} \ --Dfastqc.output_dir=${intermediatedir} \ --Dfastqc.unzip=false - -<#if seqType == "PE"> -# pair2 -fastqc ${rightbarcodefqgz} \ --Djava.io.tmpdir=${tempdir} \ --Dfastqc.output_dir=${intermediatedir} \ --Dfastqc.unzip=false - - -<#if seqType == "SR"> - putFile ${leftfastqczip} - putFile ${leftfastqcsummarytxt} - putFile ${leftfastqcsummarylog} -<#else> - putFile ${leftfastqczip} - putFile ${leftfastqcsummarytxt} - putFile ${leftfastqcsummarylog} - putFile ${rightfastqczip} - putFile ${rightfastqcsummarytxt} - putFile ${rightfastqcsummarylog} - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/FilterIndels.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/FilterIndels.ftl deleted file mode 100644 index 109f59c771..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/FilterIndels.ftl +++ /dev/null @@ -1,22 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=40:00:00 -#FOREACH externalSampleID - -inputs "${indelsbed}" -alloutputsexist "${indelsfilteredbed}" - -perl ${filterSingleSampleCallsperl} \ ---calls ${indelsbed} \ ---max_cons_av_mm 3.0 \ ---max_cons_nqs_av_mm 0.5 \ ---mode ANNOTATE \ -> ${indelsfilteredbed} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Fixmates.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Fixmates.ftl deleted file mode 100644 index 1b191aa031..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Fixmates.ftl +++ /dev/null @@ -1,31 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=6 - -inputs "${realignedbam}" -alloutputsexist \ - "${matefixedbam}" \ - "${matefixedbamindex}" - -java -jar -Xmx6g \ -${fixmateinformationjar} \ -INPUT=${realignedbam} \ -OUTPUT=${matefixedbam} \ -SORT_ORDER=coordinate \ -VALIDATION_STRINGENCY=SILENT \ -TMP_DIR=${tempdir} - -java -jar -Xmx3g ${buildbamindexjar} \ -INPUT=${matefixedbam} \ -OUTPUT=${matefixedbamindex} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Footer.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/GenomicAnnotator.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/GenomicAnnotator.ftl deleted file mode 100644 index 10e4f1bceb..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/GenomicAnnotator.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=24:00:00 mem=10 -#FOREACH externalSampleID - -inputs "${indexfile}" -inputs "${baitsbed}" -inputs "${dbsnpSNPstxt}" -inputs "${snpsvcf}" -alloutputsexist "${snpsgenomicannotatedvcf}" - -#####Annotate with dbSNP135 SNPs only##### -java -Xmx10g -jar ${genomeAnalysisTKjar} \ --T GenomicAnnotator \ --l info \ --R ${indexfile} \ --B:variant,vcf ${snpsvcf} \ --B:dbSNP135,AnnotatorInputTable ${dbsnpSNPstxt} \ --s dbSNP135.AF,dbSNP135.ASP,dbSNP135.ASS,dbSNP135.CDA,dbSNP135.CFL,dbSNP135.CLN,dbSNP135.DSS,dbSNP135.G5,\ -dbSNP135.G5A,dbSNP135.GCF,dbSNP135.GMAF,dbSNP135.GNO,dbSNP135.HD,dbSNP135.INT,dbSNP135.KGPROD,dbSNP135.KGPilot1,dbSNP135.KGPilot123,\ -dbSNP135.KGVAL,dbSNP135.LSD,dbSNP135.MTP,dbSNP135.MUT,dbSNP135.NOC,dbSNP135.NOV,dbSNP135.NS,dbSNP135.NSF,dbSNP135.NSM,dbSNP135.OM,\ -dbSNP135.OTH,dbSNP135.PH1,dbSNP135.PH2,dbSNP135.PH3,dbSNP135.PM,dbSNP135.PMC,dbSNP135.R3,dbSNP135.R5,dbSNP135.REF,dbSNP135.RSPOS,\ -dbSNP135.RV,dbSNP135.S3D,dbSNP135.SAO,dbSNP135.SCS,dbSNP135.SLO,dbSNP135.SSR,dbSNP135.SYN,dbSNP135.TPA,dbSNP135.U3,dbSNP135.U5,dbSNP135.VC,\ -dbSNP135.VLD,dbSNP135.VP,dbSNP135.WGT,dbSNP135.WTD,dbSNP135.dbSNPBuildID \ --o ${snpsgenomicannotatedvcf} \ --L ${baitsbed} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Header.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Header.ftl deleted file mode 100644 index a522b6c6fe..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Header.ftl +++ /dev/null @@ -1,11 +0,0 @@ -<#include "PBSHeader.ftl"/> - - - -# Configures the GCC bash environment -. ${root}/gcc.bashrc - -<#include "Macros.ftl"/> -<@begin/> -<#include "NGSHeader.ftl"/> -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Helpers.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/IndelGenotyper.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/IndelGenotyper.ftl deleted file mode 100644 index cf3a6c91b9..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/IndelGenotyper.ftl +++ /dev/null @@ -1,29 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=33:00:00 mem=8 -#FOREACH externalSampleID - -inputs "${mergedbam}" -inputs "${indexfile}" -alloutputsexist \ - "${indelsvcf}" \ - "${indelsbed}" \ - "${indelsverboseoutput}" - -java -Xmx8g -jar ${genomeAnalysisTKjar} \ --l INFO \ --T IndelGenotyperV2 \ --I ${mergedbam} \ --o ${indelsvcf} \ ---bedOutput ${indelsbed} \ --R ${indexfile} \ --verbose ${indelsverboseoutput} \ ---window_size 300 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Macros.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/MakeIndelMask.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/MakeIndelMask.ftl deleted file mode 100644 index bbd3c37d66..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/MakeIndelMask.ftl +++ /dev/null @@ -1,20 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=40:00:00 -#FOREACH externalSampleID - -inputs "${indelsfilteredbed}" -alloutputsexist "${indelsmaskbed}" - -python ${makeIndelMaskpyton} \ -${indelsfilteredbed} \ -10 \ -${indelsmaskbed} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Markduplicates.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Markduplicates.ftl deleted file mode 100644 index 8c1ff6737a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Markduplicates.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 - -inputs "${sortedbam}" -inputs "${sortedbamindex}" -alloutputsexist \ - "${dedupbam}" \ - "${dedupmetrics}" \ - "${dedupbamindex}" - -java -Xmx4g -jar ${markduplicatesjar} \ -INPUT=${sortedbam} \ -OUTPUT=${dedupbam} \ -METRICS_FILE=${dedupmetrics} \ -REMOVE_DUPLICATES=false \ -ASSUME_SORTED=true \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar -Xmx3g ${buildbamindexjar} \ -INPUT=${dedupbam} \ -OUTPUT=${dedupbamindex} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/MergeBam.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/MergeBam.ftl deleted file mode 100644 index 0da0e5c016..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/MergeBam.ftl +++ /dev/null @@ -1,39 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=23:59:00 mem=6 cores=2 -#FOREACH externalSampleID - -inputs <#list sortedrecalbam as srb> "${srb}" -alloutputsexist "${mergedbam}" \ -"${mergedbamindex}" - -<#if sortedrecalbam?size == 1> - #cp ${sortedrecalbam[0]} ${mergedbam} - #cp ${sortedrecalbam[0]}.bai ${mergedbamindex} - ln -s ${sortedrecalbam[0]} ${mergedbam} - ln -s ${sortedrecalbam[0]}.bai ${mergedbamindex} -<#else> - java -jar -Xmx6g ${mergesamfilesjar} \ - <#list sortedrecalbam as srb>INPUT=${srb} \ - - ASSUME_SORTED=true USE_THREADING=true \ - TMP_DIR=${tempdir} MAX_RECORDS_IN_RAM=6000000 \ - OUTPUT=${mergedbam} \ - SORT_ORDER=coordinate \ - VALIDATION_STRINGENCY=SILENT - - java -jar -Xmx3g ${buildbamindexjar} \ - INPUT=${mergedbam} \ - OUTPUT=${mergedbamindex} \ - VALIDATION_STRINGENCY=LENIENT \ - MAX_RECORDS_IN_RAM=1000000 \ - TMP_DIR=${tempdir} - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/NGSHeader.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/PBSHeader.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/PBSHeader.ftl deleted file mode 100644 index f2ee76f5a2..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/PBSHeader.ftl +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out -#PBS -W umask=0007 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/PicardQC.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/PicardQC.ftl deleted file mode 100644 index 666935b363..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/PicardQC.ftl +++ /dev/null @@ -1,117 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 - -module load picard-tools/${picardVersion} - -getFile ${sortedbam} -getFile ${indexfile} -<#if capturingKit != "None"> -getFile ${baitintervals} -getFile ${targetintervals} -<#else> - - -alloutputsexist \ - "${alignmentmetrics}" \ - "${gcbiasmetrics}" \ - "${gcbiasmetricspdf}" \ - "${insertsizemetrics}" \ - "${insertsizemetricspdf}" \ - "${meanqualitybycycle}" \ - "${meanqualitybycyclepdf}" \ - "${qualityscoredistribution}" \ - "${qualityscoredistributionpdf}" \ - "${hsmetrics}" \ - "${bamindexstats}" - - -java -jar -Xmx4g CollectAlignmentSummaryMetrics.jar \ -I=${sortedbam} \ -O=${alignmentmetrics} \ -R=${indexfile} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar CollectGcBiasMetrics.jar \ -R=${indexfile} \ -I=${sortedbam} \ -O=${gcbiasmetrics} \ -CHART=${gcbiasmetricspdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -<#if seqType == "PE"> - java -jar CollectInsertSizeMetrics.jar \ - I=${sortedbam} \ - O=${insertsizemetrics} \ - H=${insertsizemetricspdf} \ - VALIDATION_STRINGENCY=LENIENT \ - TMP_DIR=${tempdir} - - # Overwrite the PDFs that were just created by nicer onces: - ${recreateinsertsizepdfR} \ - --insertSizeMetrics ${insertsizemetrics} \ - --pdf ${insertsizemetricspdf} -<#else> - # Don't do insert size analysis because seqType != "PE" - - -java -jar MeanQualityByCycle.jar \ -I=${sortedbam} \ -O=${meanqualitybycycle} \ -CHART=${meanqualitybycyclepdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar QualityScoreDistribution.jar \ -I=${sortedbam} \ -O=${qualityscoredistribution} \ -CHART=${qualityscoredistributionpdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -<#if capturingKit != "None"> - java -jar -Xmx4g CalculateHsMetrics.jar \ - INPUT=${sortedbam} \ - OUTPUT=${hsmetrics} \ - BAIT_INTERVALS=${baitintervals} \ - TARGET_INTERVALS=${targetintervals} \ - VALIDATION_STRINGENCY=LENIENT \ - TMP_DIR=${tempdir} -<#else> - echo "## net.sf.picard.metrics.StringHeader" > ${hsmetrics} - echo "#" >> ${hsmetrics} - echo "## net.sf.picard.metrics.StringHeader" >> ${hsmetrics} - echo "#" >> ${hsmetrics} - echo "" >> ${hsmetrics} - echo "## METRICS CLASS net.sf.picard.analysis.directed.HsMetrics" >> ${hsmetrics} - echo "BAIT_SETCS CLASSGENOME_SIZE.sf.pBAIT_TERRITORY.dTARGET_TERRITORYs BAIT_DESIGN_EFFICIENCY TOTAL_READS PF_READS PF_UNIQUE_READS PCT_PF_READS PCT_PF_UQ_READS PF_UQ_READS_ALIGNED PCT_PF_UQ_READS_ALIGNED PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES ON_TARGET_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT ZERO_CVG_TARGETS_PCT FOLD_80_BASE_PENALTY PCT_TARGET_BASES_2X PCT_TARGET_BASES_10X PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X HS_LIBRARY_SIZE HS_PENALTY_1None NA_PENALNA_20X NA_PENALNA_30X NA_DROPONA NA_DROPONA NAMPLE NABRARY NAAD_GRONA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA" >> ${hsmetrics} - - -java -jar BamIndexStats.jar \ -INPUT=${sortedbam} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} \ -> ${bamindexstats} - - -putFile ${alignmentmetrics} -putFile ${gcbiasmetrics} -putFile ${gcbiasmetricspdf} -putFile ${insertsizemetrics} -putFile ${insertsizemetricspdf} -putFile ${meanqualitybycycle} -putFile ${meanqualitybycyclepdf} -putFile ${qualityscoredistribution} -putFile ${qualityscoredistributionpdf} -putFile ${hsmetrics} -putFile ${bamindexstats} diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/PicardQCrecal.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/PicardQCrecal.ftl deleted file mode 100644 index 16f296e8fc..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/PicardQCrecal.ftl +++ /dev/null @@ -1,24 +0,0 @@ -#MOLGENIS walltime=20:00:00 mem=5 - -#FOREACH externalSampleID -<#assign runtimelog = runtimelog[0] /> -<#assign fileprefix = "externalSampleID " + externalSampleID> - -###### Renaming because we call another protocol: -#inputs: -<#assign sortedbam=mergedbam /> - -#outputs: -<#assign alignmentmetrics=samplealignmentmetrics /> -<#assign gcbiasmetrics=samplegcbiasmetrics /> -<#assign gcbiasmetricspdf=samplegcbiasmetricspdf /> -<#assign insertsizemetrics=sampleinsertsizemetrics /> -<#assign insertsizemetricspdf=sampleinsertsizemetricspdf /> -<#assign meanqualitybycycle=samplemeanqualitybycycle /> -<#assign meanqualitybycyclepdf=samplemeanqualitybycyclepdf /> -<#assign qualityscoredistribution=samplequalityscoredistribution /> -<#assign qualityscoredistributionpdf=samplequalityscoredistributionpdf /> -<#assign hsmetrics=samplehsmetrics /> -<#assign bamindexstats=samplebamindexstats /> - -<#include "PicardQC.ftl"> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/QCReport.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/QCReport.ftl deleted file mode 100644 index 4e829f03df..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/QCReport.ftl +++ /dev/null @@ -1,88 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=12:34:56 mem=111111 cores=222222 -#FOREACH project -#DOCUMENTATION Documentation of QCReport.ftl, ${getStatisticsScript} - -<#include "Helpers.ftl"/> - -# We need some parameters folded per sample: -<#assign folded = foldParameters(parameters,"project,externalSampleID") /> -<#assign samplehsmetrics = stringList(folded, "samplehsmetrics") /> -<#assign samplealignmentmetrics = stringList(folded, "samplealignmentmetrics") /> -<#assign sampleinsertsizemetrics = stringList(folded, "sampleinsertsizemetrics") /> -<#assign sampleconcordancefile = stringList(folded, "sampleconcordancefile") /> -<#assign externalSampleIDfolded = stringList(folded, "externalSampleID") /> -<#assign snpsfinalvcftabletypefolded = stringList(folded, "snpsfinalvcftabletype") /> -<#assign snpsfinalvcftableclassfolded = stringList(folded, "snpsfinalvcftableclass") /> -<#assign snpsfinalvcftableimpactfolded = stringList(folded, "snpsfinalvcftableimpact") /> -<#--assign typetableoutfolded = stringList(folded, "typetableout") /> -<#assign classtableoutfolded = stringList(folded, "classtableout") /> -<#assign impacttableoutfolded = stringList(folded, "impacttableout") /--> - -# parameters in *.tex template: -<#assign samplecoverageplotpdf = stringList(folded, "samplecoverageplotpdf") /> -<#assign sampleinsertsizemetricspdf = stringList(folded, "sampleinsertsizemetricspdf") /> -<#assign samplegcbiasmetricspdf = stringList(folded, "samplegcbiasmetricspdf") /> - -inputs ${ssvQuoted(samplehsmetrics)} -inputs ${ssvQuoted(samplealignmentmetrics)} -inputs ${ssvQuoted(sampleinsertsizemetrics)} -inputs ${ssvQuoted(dedupmetrics)} -inputs ${ssvQuoted(sampleconcordancefile)} -inputs ${qcstatisticscolnames} - -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -# get general sample statistics -Rscript ${getStatisticsScript} \ ---hsmetrics ${csvQuoted(samplehsmetrics)} \ ---alignment ${csvQuoted(samplealignmentmetrics)} \ ---insertmetrics ${csvQuoted(sampleinsertsizemetrics)} \ ---dedupmetrics ${csvQuoted(dedupmetrics)} \ ---concordance ${csvQuoted(sampleconcordancefile)} \ ---sample ${csvQuoted(externalSampleIDfolded)} \ ---colnames ${qcstatisticscolnames} \ ---csvout ${qcstatisticscsv} \ ---tableout ${qcstatisticstex} \ ---descriptionout ${qcstatisticsdescription} \ ---baitsetout ${qcbaitset} \ ---qcdedupmetricsout ${qcdedupmetricsout} - -# get dedup info per flowcell-lane-barcode/sample -Rscript ${getDedupInfoScript} \ ---dedupmetrics ${csvQuoted(dedupmetrics)} \ ---flowcell ${csvQuoted(flowcell)} \ ---lane ${csvQuoted(lane)} \ ---sample ${csvQuoted(externalSampleID)} \ ---paired TRUE \ ---qcdedupmetricsout "${qcdedupmetricsout}" - -# get snp stats per sample -Rscript ${createsnptablescript} \ ---sample ${csvQuoted(externalSampleIDfolded)} \ ---type ${csvQuoted(snpsfinalvcftabletypefolded)} \ ---class ${csvQuoted(snpsfinalvcftableclassfolded)} \ ---impact ${csvQuoted(snpsfinalvcftableimpactfolded)} \ ---typetableout "${typetableout}" \ ---classtableout "${classtableout}" \ ---impacttableout "${impacttableout}" - - -# create workflow figure -echo "${graph(workflowElements)}" | ${dot} -Tpng > ${workflowpng} - -# save latex template in file -echo "<#include "QCReportTemplate.tex"/>" > ${qcstatisticstexreport} - -pdflatex -output-directory=${qcdir} ${qcstatisticstexreport} -pdflatex -output-directory=${qcdir} ${qcstatisticstexreport} <#--do twice to fill all cross references--> diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/QCReportBUG.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/QCReportBUG.ftl deleted file mode 100644 index e338dc1c32..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/QCReportBUG.ftl +++ /dev/null @@ -1,11 +0,0 @@ -#MOLGENIS walltime=00:05:00 -#FOREACH project -#DOCUMENTATION Documentation of QCReport.ftl, ${getStatisticsScript} - -<#include "Helpers.ftl"/> - -# We need some parameters folded per sample: -Parameters: -${parameters} - -<#assign folded = foldParameters(parameters,"project,externalSampleID") /> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/QCReportTemplate.tex b/modules/compute/demo/debugFolding/inputdir/protocols/QCReportTemplate.tex deleted file mode 100644 index ce3306d522..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/QCReportTemplate.tex +++ /dev/null @@ -1,162 +0,0 @@ -\documentclass[a4paper,12pt]{article} -\usepackage{nameref} -\usepackage{grffile} -\usepackage{graphicx} -\usepackage[strings]{underscore} -\usepackage{verbatim} -\usepackage{wrapfig} -\usepackage{lastpage} - -\begin{comment} -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# -\end{comment} - -\newenvironment{narrow}[2]{ - \begin{list}{}{ - \setlength{\leftmargin}{#1} - \setlength{\rightmargin}{#2} - \setlength{\listparindent}{\parindent} - \setlength{\itemindent}{\parindent} - \setlength{\parsep}{\parskip} - } - \item[] -}{\end{list}} - -\title{Next Generation Sequencing report} -\author{\small Genome Analysis Facility (GAF), Genomics Coordination Centre (GCC)\\\\ -\small University Medical Centre Groningen} - -\begin{document} -\maketitle -\thispagestyle{empty} -\vspace{40mm} - -\begin{table}[h] - \centering - \begin{tabular}{l l} - \hline - \multicolumn{2}{l}{\textbf{Report}} \\\\ - Created on & \today \\\\ - Number of pages & \\pageref{LastPage} \\\\ \\\\ - Generated by & MOLGENIS Compute \\\\ - \\\\ - \multicolumn{2}{l}{\textbf{Project}} \\\\ - Project name & ${project} \\\\ - Number of samples & ${samplecoverageplotpdf?size} \\\\ - \\\\ - \multicolumn{2}{l}{\textbf{Customer}} \\\\ - Principal investigator & ${contact?replace("<", "/ ")?replace(">", "")} \\\\ - \\\\ - \multicolumn{2}{l}{\textbf{Contact}} \\\\ - Name & Cleo C. van Diemen \\\\ - E-mail & c.c.van.diemen@umcg.nl \\\\ - \hline - \end{tabular} -\end{table} - -\clearpage -\tableofcontents - -\clearpage -\section*{Introduction} -\addcontentsline{toc}{section}{Introduction} -This report describes a series of statistics about your sequencing data. Together with this report you'll receive a SNP-list. If you, in addition, also want the raw data, then please notify us via e-mail. In any case we'll delete the raw data, three months after \today. - -\clearpage -\section*{Project analysis results} -\addcontentsline{toc}{section}{Project analysis results} - -\subsection*{Overview statistics} -\addcontentsline{toc}{subsection}{Overview statistics} -\label{subsect:overviewstatistics} -% statistics table -\input{${qcstatisticstex}} - -\begin{minipage}{\textwidth} - Name of the bait set(s) used in the hybrid selection for this project:\\\\ - \textbf{\input{${qcbaitset}}} -\end{minipage} - -\clearpage -\subsection*{Description statistics table} -\addcontentsline{toc}{subsection}{Description statistics table} -\begin{table}[h!] - \centering - \begin{tabular}{r p{12cm}} - \input{${qcstatisticsdescription}} - \end{tabular} -\end{table} - -\clearpage -\subsection*{Capturing} -\addcontentsline{toc}{subsection}{Capturing} -The following figures show the cumulative depth distribution in the target regions that are located on \emph{chromosome 1}. The fractions of bases that is covered with at least 10x, 20x and 30x are marked with a dot. Please see section \"\\nameref{subsect:overviewstatistics}\" for the full coverage statistics per sample; \emph{i.e.}, in the target regions on \emph{all chromosomes}. -${figures(samplecoverageplotpdf)} - -\clearpage -\subsection*{Insert size distribution} -\addcontentsline{toc}{subsection}{Insert size distribution} -The following figures show the insert size distribution per sample. Insert refers to the base pairs that are ligated between the adapters. -${figures(sampleinsertsizemetricspdf)} - -%\clearpage -%\subsection*{Demultiplex statistics} -%\addcontentsline{toc}{subsection}{Demultiplex statistics} -%Under construction... -%displaystats(demultiplexstats) - -%\clearpage -%\subsection*{GC metrics} -%\addcontentsline{toc}{subsection}{GC metrics} -%The following figures show the GC-content distribution per sample. -%${figures(samplegcbiasmetricspdf)} - -%\clearpage -%\subsection*{SNP statistics} -%\addcontentsline{toc}{subsection}{SNP statistics} -%The tables with caption 'Functional type', 'Functional class' and 'Functional impact', classify the SNPs, based on Ensembl, build 37.64. -%\input{${typetableout}} -%\input{${classtableout}} -%\input{${impacttableout}} - -\clearpage -\subsection*{Duplication rates} -\addcontentsline{toc}{subsection}{Duplication rates} -\input{${qcdedupmetricsout}} - -\clearpage -\section*{Appendix 1: Genome Analysis Facility Pipeline} -\addcontentsline{toc}{section}{Appendix 1: Genome Analysis Facility Pipeline} -\subsection*{Exome sequencing} -\addcontentsline{toc}{subsection}{Exome sequencing} -\begin{wrapfigure}{r}{0.5\textwidth} - \begin{center} - \includegraphics[width=.5\textwidth]{${gaffig}} - \end{center} - \caption{Workflow in the lab} - \label{fig:wet} -\end{wrapfigure} -Figure \ref{fig:wet} illustrated the basic experimental process of exome capture sequencing. The Genomic DNA sample was randomly fragmented using Nebulisation. Then barcoded adapters were ligated to both ends of the resulting fragments, according the standard New England Biolabs protocol. Fragments with an insert size of 220 bp on average were excised using the Caliper XT gel system and the extracted DNA was amplified with PCR. - -The quality of the product was verified on the BioRad Experion instrument. If the quality of the product meets the criteria, the product is multiplexed in an equimolar pool of 4 simular products. This pool is hybridized to the Agilent SureSelect All exon V2, according the provided protocol. After amplification of the enriched products with PCR the quality of the products is verified on the BioRad Experion instrument and Paired End sequenced on the HiSeq2000 with 100 bp reads. Image Files were processed using standard Illumina basecalling software and the generated reads are ready for downstream processing after demultiplexing. - -\clearpage -\section*{Appendix 2: Bioinformatics pipeline} -\addcontentsline{toc}{section}{Appendix 2: Bioinformatics pipeline} -Your samples have been anlayzed with bioinformatics pipeline shown in Figure \ref{fig:dry}. -\begin{figure}[h] - \caption{Bioinformatics pipeline. The ovals describe the steps in the pipeline. The arrows indicate the work flow of data between the steps.} - \begin{center} - \includegraphics[width=.9\textwidth]{${workflowpng}} - \end{center} - \label{fig:dry} -\end{figure} -\end{document} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Realign.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Realign.ftl deleted file mode 100644 index c3f28c606b..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Realign.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=10 cores=1 - - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -inputs "${realignTargets}" -alloutputsexist "${realignedbam}" - -java -Djava.io.tmpdir=${tempdir} -Xmx10g -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T IndelRealigner \ --U ALLOW_UNINDEXED_BAM \ --I ${dedupbam} \ ---out ${realignedbam} \ --targetIntervals ${realignTargets} \ --R ${indexfile} \ --D ${dbsnprod} \ --B:indels,VCF ${pilot1KgVcf} \ --knownsOnly \ --LOD 0.4 \ --maxReads 2000000 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/RealignTargetCreator.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/RealignTargetCreator.ftl deleted file mode 100644 index f9e3dd409f..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/RealignTargetCreator.ftl +++ /dev/null @@ -1,29 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=10 - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -alloutputsexist \ - "${realignTargets}" - -java -Xmx10g -jar -Djava.io.tmpdir=${tempdir} \ -${genomeAnalysisTKjar} \ --l INFO \ --T RealignerTargetCreator \ --U ALLOW_UNINDEXED_BAM \ --I ${dedupbam} \ --R ${indexfile} \ --D ${dbsnprod} \ --B:indels,VCF ${pilot1KgVcf} \ --o ${realignTargets} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Recalibrate.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Recalibrate.ftl deleted file mode 100644 index d9a474fcd5..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Recalibrate.ftl +++ /dev/null @@ -1,26 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:59:00 mem=4 cores=1 - -inputs "${indexfile}" -inputs "${matefixedbam}" -inputs "${matefixedcovariatecsv}" -alloutputsexist "${recalbam}" - -java -jar -Xmx4g \ -${genomeAnalysisTKjar} \ --l INFO \ --T TableRecalibration \ --U ALLOW_UNINDEXED_BAM \ --R ${indexfile} \ --I ${matefixedbam} \ ---recal_file ${matefixedcovariatecsv} \ ---out ${recalbam} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/RunGerald.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/RunGerald.ftl deleted file mode 100644 index 6e4d1f5a91..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/RunGerald.ftl +++ /dev/null @@ -1,20 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:59:00 mem=12 cores=8 -#FOREACH run - -#Source GAF bash -. ${gafhome}/gaf.bashrc - - -perl ${gafscripts}/run_GERALD.pl \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/SamSort.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/SamSort.ftl deleted file mode 100644 index b93fd1e474..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/SamSort.ftl +++ /dev/null @@ -1,37 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 -#TARGETS - -module load picard-tools/${picardVersion} - -getFile ${bamfile} -alloutputsexist \ - "${sortedbam}" \ - "${sortedbamindex}" - -java -jar -Xmx3g SortSam.jar \ -INPUT=${bamfile} \ -OUTPUT=${sortedbam} \ -SORT_ORDER=coordinate \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} - -java -jar -Xmx3g BuildBamIndex.jar \ -INPUT=${sortedbam} \ -OUTPUT=${sortedbamindex} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} - -putFile ${sortedbam} -putFile ${sortedbamindex} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/SamSortRecal.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/SamSortRecal.ftl deleted file mode 100644 index 6662ebb180..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/SamSortRecal.ftl +++ /dev/null @@ -1,7 +0,0 @@ -#MOLGENIS walltime=35:59:00 mem=4 - -<#assign bamfile=recalbam /> -<#assign sortedbam=sortedrecalbam /> -<#assign sortedbamindex=sortedrecalbamindex /> - -<#include "SamSort.ftl" /> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/SamToBam.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/SamToBam.ftl deleted file mode 100644 index b6515625fd..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/SamToBam.ftl +++ /dev/null @@ -1,26 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=3 -#TARGETS - -module load picard-tools/${picardVersion} - -getFile ${samfile} -alloutputsexist "${bamfile}" - -java -jar -Xmx3g SamFormatConverter.jar \ -INPUT=${samfile} \ -OUTPUT=${bamfile} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=2000000 \ -TMP_DIR=${tempdir} - -putFile ${bamfile} diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Submit.sh.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Submit.sh.ftl deleted file mode 100644 index 036ea93daf..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Submit.sh.ftl +++ /dev/null @@ -1,11 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 0 - - -touch $DIR/${workflowfilename}.finished \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/UnifiedGenotyper.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/UnifiedGenotyper.ftl deleted file mode 100644 index 1d18d834e8..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/UnifiedGenotyper.ftl +++ /dev/null @@ -1,32 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=46:00:00 mem=8 cores=5 -#FOREACH externalSampleID - -inputs "${mergedbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -alloutputsexist \ - "${snpsvcf}" \ - "${snpsvcf}.metrics" - -java -Xmx8g -Djava.io.tmpdir=${tempdir} -XX:+UseParallelGC -XX:ParallelGCThreads=1 -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T UnifiedGenotyper \ --I ${mergedbam} \ ---out ${sample}.snps.vcf \ --R ${indexfile} \ --D ${dbsnprod} \ --stand_call_conf 30.0 \ --stand_emit_conf 10.0 \ --nt 4 \ ---metrics_file ${sample}.snps.vcf.metrics \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/VQSRApplyRecal.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/VQSRApplyRecal.ftl deleted file mode 100644 index 2ae94dac00..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/VQSRApplyRecal.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/Realign.ftl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: pneerincx $ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=10 cores=1 - - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -inputs "${realignTargets}" -alloutputsexist "${realignedbam}" - -java -Djava.io.tmpdir=${tempdir} -Xmx10g -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T IndelRealigner \ --U ALLOW_UNINDEXED_BAM \ --I ${dedupbam} \ ---out ${realignedbam} \ --targetIntervals ${realignTargets} \ --R ${indexfile} \ --D ${dbsnprod} \ --B:indels,VCF ${pilot1KgVcf} \ --knownsOnly \ --LOD 0.4 \ --maxReads 2000000 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/VQSRVariantRecal.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/VQSRVariantRecal.ftl deleted file mode 100644 index 2072c4713e..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/VQSRVariantRecal.ftl +++ /dev/null @@ -1,33 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/Realign.ftl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: pneerincx $ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 cores=1 - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -inputs "${realignTargets}" -alloutputsexist "${realignedbam}" - -java -Djava.io.tmpdir=${tempdir} -Xmx4g -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T VariantRecalibrator \ --R ${indexfile} \ - -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \ - -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ - -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \ - -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_132.b37.vcf \ --B:concordantSet,VCF,known=true,training=true,truth=true,prior=10.0 path/to/concordantSet.vcf - -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ \ - -recalFile path/to/output.recal \ - -tranchesFile path/to/output.tranches \ - -rscriptFile path/to/output.plots.R diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/VariantAnnotator.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/VariantAnnotator.ftl deleted file mode 100644 index 4d0abeaadf..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/VariantAnnotator.ftl +++ /dev/null @@ -1,48 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:00:00 mem=10 -#FOREACH externalSampleID - -inputs "${snpeffjar}" -inputs "${snpeffconfig}" -inputs "${snpsgenomicannotatedvcf}" -inputs "${mergedbam}" -inputs "${dbsnpvcf}" -inputs "${indexfile}" -<#if capturingKit != "None">inputs "${baitsbed}" -alloutputsexist "${snpeffsummaryhtml}" "${snpeffintermediate}" "${snpsfinalvcf}" - -####Create snpEFF annotations on original input file#### -java -Xmx4g -jar ${snpeffjar} \ -eff \ --v \ --c ${snpeffconfig} \ --i vcf \ --o vcf \ -GRCh37.64 \ --onlyCoding true \ --stats ${snpeffsummaryhtml} \ -${snpsgenomicannotatedvcf} \ -> ${snpeffintermediate} - -####Annotate SNPs with snpEff information#### -java -jar -Xmx4g ${genomeAnalysisTKjar1411} \ --T VariantAnnotator \ ---useAllAnnotations \ ---excludeAnnotation MVLikelihoodRatio \ ---excludeAnnotation TechnologyComposition \ --I ${mergedbam} \ ---snpEffFile ${snpeffintermediate} \ --D ${dbsnpvcf} \ --R ${indexfile} \ ---variant ${snpsgenomicannotatedvcf} \<#if capturingKit != "None"> --L ${baitsbed} \ --o ${snpsfinalvcf} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/VariantFiltration.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/VariantFiltration.ftl deleted file mode 100644 index f495685fbe..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/VariantFiltration.ftl +++ /dev/null @@ -1,58 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:00:00 mem=10 -inputs "${snpsgenomicannotatedvcf}" -inputs "${indelsmaskbed}" -inputs "${indexfile}" -<#if capturingKit != "None">inputs "${baitintervals}" -inputs "${dbsnprod}" -alloutputsexist "${snpsgenomicannotatedfilteredvcf}" - -rm ${snpsgenomicannotatedvcf}.idx - -## -# http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v2 -## -# HARD_TO_VALIDATE: more than 10% (or more than 3) of the reads have mapping quality 0 -# MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1) -## -# "Note that For exomes, a straight DP filter shouldn't be used because the -# relationship between misalignments and depth isn't clear for capture data. -# Note that as of Dec. 2010 we no longer recommend using AB to filter, as (1) -# it's not generated by the UG by default any more and (2) QD is a better, -# and largely equivalent, filter." -# QUAL < 30.0 || QD < 5.0 || HRun > 5 || SB > -0.10 -# The UG itself: the confidence score and emission thresholds (-stand_call_conf -# and -stand_emit_conf, both Phredscores) are chosen based on the (expected) -# overall coverage. Anything below the emission threshold is not called, -# anything between the two thresholds is flagged LowQual. -# To discuss: a straight DP filter, set to 5 or 10? Or higher? Why, why not? -# For now, I'll include an expression to mark SNPs with a depth of 10 or higher -# with "DEPTH_10". -## - -java -jar -Xmx10g ${genomeAnalysisTKjar} \ --l INFO \ --T VariantFiltration \ --B:variant,VCF ${snpsgenomicannotatedvcf} \ --B:mask,Bed ${indelsmaskbed} \ --R ${indexfile} \<#if capturingKit != "None"> --L ${baitintervals} \ --D ${dbsnprod} \ --o ${snpsgenomicannotatedfilteredvcf} \ ---maskName InDel \ ---clusterWindowSize 10 \ ---filterExpression "QUAL < 30.0 || QD < 5.0 || HRun > 5 || SB > -0.10" \ ---filterName GATK_EXOME_standard \ ---filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \ ---filterName "HARD_TO_VALIDATE" \ ---filterExpression "DP > 10" \ ---filterName "DEPTH_10" \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/VcfToTable.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/VcfToTable.ftl deleted file mode 100644 index 289c6fa893..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/VcfToTable.ftl +++ /dev/null @@ -1,43 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:40:00 -#FOREACH externalSampleID - -inputs "${snpsfinalvcf}" -alloutputsexist "${snpsfinalvcftable}" "${snpsfinalvcftabletype}" "${snpsfinalvcftableclass}" "${snpsfinalvcftableimpact}" - -####Transform VCF file into tabular file#### -python ${vcf2tablepy} \ -${snpsfinalvcf} \ --f CHROM,POS,ID,REF,ALT,QUAL,FILTER,AB,AC,AF,ALTFWD,ALTREV,AN,\ -BaseCounts,BaseQRankSum,DB,DP,DS,Dels,FS,GC,HRun,HW,HaplotypeScore,\ -LowMQ,MQ,MQ0,MQ0Fraction,MQRankSum,PercentNBaseSolid,QD,ReadPosRankSum,REFFWD,REFREV,SB,SBD,\ -SNPEFF_AMINO_ACID_CHANGE,SNPEFF_CODON_CHANGE,SNPEFF_EFFECT,SNPEFF_EXON_ID,SNPEFF_FUNCTIONAL_CLASS,\ -SNPEFF_GENE_BIOTYPE,SNPEFF_GENE_NAME,SNPEFF_IMPACT,SNPEFF_TRANSCRIPT_ID,Samples,TDT,\ -dbSNP132.AF,dbSNP132.ASP,dbSNP132.ASS,dbSNP132.CDA,dbSNP132.CFL,dbSNP132.CLN,dbSNP132.DSS,dbSNP132.G5,\ -dbSNP132.G5A,dbSNP132.GCF,dbSNP132.GMAF,dbSNP132.GNO,dbSNP132.HD,dbSNP132.INT,dbSNP132.KGPROD,dbSNP132.KGPilot1,dbSNP132.KGPilot123,\ -dbSNP132.KGVAL,dbSNP132.LSD,dbSNP132.MTP,dbSNP132.MUT,dbSNP132.NOC,dbSNP132.NOV,dbSNP132.NS,dbSNP132.NSF,dbSNP132.NSM,dbSNP132.OM,\ -dbSNP132.OTH,dbSNP132.PH1,dbSNP132.PH2,dbSNP132.PH3,dbSNP132.PM,dbSNP132.PMC,dbSNP132.R3,dbSNP132.R5,dbSNP132.REF,dbSNP132.RSPOS,\ -dbSNP132.RV,dbSNP132.S3D,dbSNP132.SAO,dbSNP132.SCS,dbSNP132.SLO,dbSNP132.SSR,dbSNP132.SYN,dbSNP132.TPA,dbSNP132.U3,dbSNP132.U5,dbSNP132.VC,\ -dbSNP132.VLD,dbSNP132.VP,dbSNP132.WGT,dbSNP132.WTD,dbSNP132.dbSNPBuildID,\ -sumGLbyD,\ -FORMAT,${externalSampleID} \ --o ${snpsfinalvcftable} - -# get SNP statistics -perl ${snpannotationstatspl} \ --vcf_table ${snpsfinalvcftable} \ --typefile ${snpsfinalvcftabletype} \ --classfile ${snpsfinalvcftableclass} \ --impactfile ${snpsfinalvcftableimpact} \ --snptypes DOWNSTREAM,INTERGENIC,INTRAGENIC,INTRON,NON_SYNONYMOUS_CODING,NON_SYNONYMOUS_START,SPLICE_SITE_ACCEPTOR,SPLICE_SITE_DONOR,START_GAINED,START_LOST,STOP_GAINED,STOP_LOST,SYNONYMOUS_CODING,SYNONYMOUS_STOP,UPSTREAM,UTR_3_PRIME,UTR_5_PRIME \ --snpclasses MISSENSE,NONSENSE,NONE,SILENT \ --snpimpacts HIGH,LOW,MODERATE,MODIFIER \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/Zipfq.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/Zipfq.ftl deleted file mode 100644 index f925242287..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/Zipfq.ftl +++ /dev/null @@ -1,28 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=10:00:00 nodes=1 cores=1 mem=10 - -<#if seqType == "SR"> - # assume single read - alloutputsexist ${leftbarcodefqgz} - inputs ${leftbarcodefq} -<#else> - # assume paired end - alloutputsexist ${leftbarcodefqgz} ${rightbarcodefqgz} - inputs ${leftbarcodefq} ${rightbarcodefq} - - -# The following code gzips files and removes original file -# However, in the case of a symlink, the symlink is removed. - gzip -f ${leftbarcodefq} -<#if seqType == "PE"> - gzip -f ${rightbarcodefq} - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/getdata_original.sh b/modules/compute/demo/debugFolding/inputdir/protocols/getdata_original.sh deleted file mode 100644 index 03d178d362..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/getdata_original.sh +++ /dev/null @@ -1,102 +0,0 @@ -#!/bin/bash - -getdata() -{ -CLUSTER="cluster"; -GRID="grid"; - -INPUT="input"; -OUTPUT="output"; -EXE="exe"; - -ARGS=($@) -BACKEND="${ARGS[0]}"; -OPERATION="${ARGS[1]}"; - -NUMBER="${#ARGS[@]}"; -MIN=4 - -if [ "$NUMBER" -gt "$MIN" ] -then - - for (( i=4; i<$#; i++ )) - do - value="${ARGS[2]}${ARGS[3]}${ARGS[$i]}"; - - if [ "$BACKEND" == "$CLUSTER" ] - then - #check if data exists on the cluster - if test ! -e $value; - then - echo "$value is missing" 1>&2 - fi - fi - - if [ "$BACKEND" == "$GRID" ] - then - #download/upload data on the grid - if [ "$OPERATION" == "$INPUT" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]}${ARGS[$i]} - fi - - if [ "$OPERATION" == "$OUTPUT" ] - then - lcg-cr -l lfn://grid$value file:///$TMPDIR/${INPUTS[2]}${INPUTS[$i]} - fi - - #download executable - if [ "$OPERATION" == "$EXE" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]}${ARGS[$i]} - chmod 755 $TMPDIR${ARGS[3]}${ARGS[$i]} - fi - - #check sum on the execution node - echo -n "SUM_ADLER32_${ARGS[3]}${ARGS[$i]} " - adler32 file:///$TMPDIR${ARGS[3]}${ARGS[$i]} - fi - - done - -else - - if [ "$BACKEND" == "$CLUSTER" ] - then - #check if data exists on the cluster - if test ! -e $value; - then - echo "$value is missing" 1>&2 - fi - fi - - if [ "$BACKEND" == "$GRID" ] - then - #download/upload data on the grid - if [ "$OPERATION" == "$INPUT" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]} - fi - - if [ "$OPERATION" == "$OUTPUT" ] - then - lcg-cr -l lfn://grid$value file:///$TMPDIR/${INPUTS[2]} - fi - - #download executable - if [ "$OPERATION" == "$EXE" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]} - chmod 755 $TMPDIR${ARGS[3]} - fi - - #check sum on the execution node - echo -n "SUM_ADLER32_${ARGS[3]}${ARGS[$i]} " - adler32 file:///$TMPDIR${ARGS[3]} - fi - -fi - -} - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/gwas/FixColumns.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/gwas/FixColumns.ftl deleted file mode 100644 index 4d50601658..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/gwas/FixColumns.ftl +++ /dev/null @@ -1,53 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:10:00 -#FOREACH project - -# -# Change permissions. -# -umask 0007 - -# -# Create project dirs. -# -mkdir -p ${projectRawDataDir} -mkdir -p ${projectJobsDir} -mkdir -p ${projectLogsDir} -mkdir -p ${projectIntermediateDir} -mkdir -p ${projectResultsDir} - -<#if familyIDs?exists> - ${plink} --noweb --silent \ - --bfile ${plinkFileRaw} \ - --update-ids ${familyIDs} \ - --make-bed --out ${plinkFileFixedFamilies} -<#else> - ln -s ${plinkFileRaw} ${plinkFileFixedFamilies} - - -<#if parentIDs?exists> - ${plink} --noweb --silent \ - --bfile ${plinkFileFixedFamilies} \ - --update-parents ${parentIDs} \ - --make-bed --out ${plinkFileFixedParents} -<#else> - ln -s ${plinkFileFixedFamilies} ${plinkFileFixedParents} - - -<#if removeIDs?exists> - ${plink} --noweb --silent \ - --bfile ${plinkFileFixedParents} \ - --remove ${removeIDs} \ - --make-bed --out ${plinkFileClean} -<#else> - ln -s ${plinkFileFixedParents} ${plinkFileClean} - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/CustomSubmit.sh.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Footer.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Header.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Header.ftl deleted file mode 100644 index 56d943bf8a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Header.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#!/bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - - - - - -# Configures the GCC bash environment -. ${root}/gcc.bashrc - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Helpers.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Macros.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/beagleOutputToTrityper.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/beagleOutputToTrityper.ftl deleted file mode 100644 index 3a210abc9d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/beagleOutputToTrityper.ftl +++ /dev/null @@ -1,18 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS imputedoutputbeagle #<-- Add gprobsinput later -#OUTPUTS bgltotrityperoutput -#EXES plink -#TARGETS project,chr - -inputs "${imputedoutputbeagle}" -alloutputsexist "${bgltotrityperoutput}" #<-- Check all beagle outputs, where does the inserted chrnum come from?? - - - -#Convert beagle output to TriTyper format using hacked converter from Harm-Jan (This should be fixed by TriTyper team/developers) -java -jar -Xmx4g ${convertbgltotrityperjar} \ -/target/gpfs2/gcc/home/pdeelen/beagleImputed/imputed.chr20.chr20.bgl.gprobs.gz \ #<-- Change this when known where chrnum is coming from -${bgltotrityperoutput} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createBglFileFromPlinkData.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createBglFileFromPlinkData.ftl deleted file mode 100644 index bb20ba1857..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createBglFileFromPlinkData.ftl +++ /dev/null @@ -1,16 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS plinkdatatransposed -#OUTPUTS beaglefile -#EXES -#TARGETS project,chr - -inputs "${plinkdatatransposed}.tped" -alloutputsexist "${beaglefile}" - -#Create beagle format file to be used for reference (GoNL) beagle phased data -gawk '{$2=$1":"$4; $1="M"; $3=""; $4=""; print $0}' \ -${plinkdatatransposed}.tped \ -> ${beaglefile} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createImputationScripts/sampleWorksheet.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createImputationScripts/sampleWorksheet.csv deleted file mode 100644 index e5f02f2ae1..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createImputationScripts/sampleWorksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,studyInputDir,referencePanel,imputationResultDir,imputationPipeline,genomeBuild -1240Blood_b37,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood_b37/,gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/testImputations/1240Blood_b37Impute2,impute2,b37 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createMarkerFile.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createMarkerFile.ftl deleted file mode 100644 index acb7f484d0..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/createMarkerFile.ftl +++ /dev/null @@ -1,55 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS plinkdatatransposed -#OUTPUTS beaglefile -#EXES plink -#TARGETS project,chr - -#inputs "${plinkdatatransposed}.tped" -#alloutputsexist "${plinkdatatransposed}.frq" -#alloutputsexist "${plinkdatatransposed}.log" -#alloutputsexist "${markers}" - - -#Create first part of marker file for beagle -${plink} \ ---tfile ${plinkdatatransposed} \ ---freq \ ---out ${plinkdatatransposed} \ ---noweb - -gawk '$1!="CHR" {print $2,$3,$4}' ${plinkdatatransposed}.frq \ -> ${markerspt1} - - -#Create second part of markers -${plink} \ ---tfile ${plinkdatatransposed} \ ---recode \ ---out ${plinkdata} \ ---noweb - -gawk '{print $2,$4,$1":"$4}' ${plinkdata}.map \ -> ${markerspt2} - - -#Join both markerfiles merging via IDs -join -1 1 -2 1 \ -${markerspt1} \ -${markerspt2} \ -| gawk '{print $5,$4,$2,$3}' \ -> ${markers} #<- define this later when method is finished (include step from perl scripts) - -#####ADD rest of template when steps are exactly known###### - -#vcftools -> --keep-filtered PASS - -#--non-ref-af -#--max-non-ref-af - - - -# Read GoNL vcf, extract lines starting with chrnumber, check alt allele for . If alt allele doesn't contain a . print marker file -#grep -P '^20.+' gonl.chr20.release3.vcf | awk '{ if($5!=".") {print $1":"$2,$2,$4,$5}}' \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37AllChrBins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37AllChrBins.csv deleted file mode 100644 index 6032e406d7..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37AllChrBins.csv +++ /dev/null @@ -1,590 +0,0 @@ -chr,fromChrPos,toChrPos -1,1,5000001 -1,5000001,10000001 -1,10000001,15000001 -1,15000001,20000001 -1,20000001,25000001 -1,25000001,30000001 -1,30000001,35000001 -1,35000001,40000001 -1,40000001,45000001 -1,45000001,50000001 -1,50000001,55000001 -1,55000001,60000001 -1,60000001,65000001 -1,65000001,70000001 -1,70000001,75000001 -1,75000001,80000001 -1,80000001,85000001 -1,85000001,90000001 -1,90000001,95000001 -1,95000001,100000001 -1,100000001,105000001 -1,105000001,110000001 -1,110000001,115000001 -1,115000001,120000001 -1,120000001,125000001 -1,125000001,130000001 -1,130000001,135000001 -1,135000001,140000001 -1,140000001,145000001 -1,145000001,150000001 -1,150000001,155000001 -1,155000001,160000001 -1,160000001,165000001 -1,165000001,170000001 -1,170000001,175000001 -1,175000001,180000001 -1,180000001,185000001 -1,185000001,190000001 -1,190000001,195000001 -1,195000001,200000001 -1,200000001,205000001 -1,205000001,210000001 -1,210000001,215000001 -1,215000001,220000001 -1,220000001,225000001 -1,225000001,230000001 -1,230000001,235000001 -1,235000001,240000001 -1,240000001,245000001 -1,245000001,250000001 -2,1,5000001 -2,5000001,10000001 -2,10000001,15000001 -2,15000001,20000001 -2,20000001,25000001 -2,25000001,30000001 -2,30000001,35000001 -2,35000001,40000001 -2,40000001,45000001 -2,45000001,50000001 -2,50000001,55000001 -2,55000001,60000001 -2,60000001,65000001 -2,65000001,70000001 -2,70000001,75000001 -2,75000001,80000001 -2,80000001,85000001 -2,85000001,90000001 -2,90000001,95000001 -2,95000001,100000001 -2,100000001,105000001 -2,105000001,110000001 -2,110000001,115000001 -2,115000001,120000001 -2,120000001,125000001 -2,125000001,130000001 -2,130000001,135000001 -2,135000001,140000001 -2,140000001,145000001 -2,145000001,150000001 -2,150000001,155000001 -2,155000001,160000001 -2,160000001,165000001 -2,165000001,170000001 -2,170000001,175000001 -2,175000001,180000001 -2,180000001,185000001 -2,185000001,190000001 -2,190000001,195000001 -2,195000001,200000001 -2,200000001,205000001 -2,205000001,210000001 -2,210000001,215000001 -2,215000001,220000001 -2,220000001,225000001 -2,225000001,230000001 -2,230000001,235000001 -2,235000001,240000001 -2,240000001,245000001 -3,1,5000001 -3,5000001,10000001 -3,10000001,15000001 -3,15000001,20000001 -3,20000001,25000001 -3,25000001,30000001 -3,30000001,35000001 -3,35000001,40000001 -3,40000001,45000001 -3,45000001,50000001 -3,50000001,55000001 -3,55000001,60000001 -3,60000001,65000001 -3,65000001,70000001 -3,70000001,75000001 -3,75000001,80000001 -3,80000001,85000001 -3,85000001,90000001 -3,90000001,95000001 -3,95000001,100000001 -3,100000001,105000001 -3,105000001,110000001 -3,110000001,115000001 -3,115000001,120000001 -3,120000001,125000001 -3,125000001,130000001 -3,130000001,135000001 -3,135000001,140000001 -3,140000001,145000001 -3,145000001,150000001 -3,150000001,155000001 -3,155000001,160000001 -3,160000001,165000001 -3,165000001,170000001 -3,170000001,175000001 -3,175000001,180000001 -3,180000001,185000001 -3,185000001,190000001 -3,190000001,195000001 -3,195000001,200000001 -4,1,5000001 -4,5000001,10000001 -4,10000001,15000001 -4,15000001,20000001 -4,20000001,25000001 -4,25000001,30000001 -4,30000001,35000001 -4,35000001,40000001 -4,40000001,45000001 -4,45000001,50000001 -4,50000001,55000001 -4,55000001,60000001 -4,60000001,65000001 -4,65000001,70000001 -4,70000001,75000001 -4,75000001,80000001 -4,80000001,85000001 -4,85000001,90000001 -4,90000001,95000001 -4,95000001,100000001 -4,100000001,105000001 -4,105000001,110000001 -4,110000001,115000001 -4,115000001,120000001 -4,120000001,125000001 -4,125000001,130000001 -4,130000001,135000001 -4,135000001,140000001 -4,140000001,145000001 -4,145000001,150000001 -4,150000001,155000001 -4,155000001,160000001 -4,160000001,165000001 -4,165000001,170000001 -4,170000001,175000001 -4,175000001,180000001 -4,180000001,185000001 -4,185000001,190000001 -4,190000001,195000001 -5,1,5000001 -5,5000001,10000001 -5,10000001,15000001 -5,15000001,20000001 -5,20000001,25000001 -5,25000001,30000001 -5,30000001,35000001 -5,35000001,40000001 -5,40000001,45000001 -5,45000001,50000001 -5,50000001,55000001 -5,55000001,60000001 -5,60000001,65000001 -5,65000001,70000001 -5,70000001,75000001 -5,75000001,80000001 -5,80000001,85000001 -5,85000001,90000001 -5,90000001,95000001 -5,95000001,100000001 -5,100000001,105000001 -5,105000001,110000001 -5,110000001,115000001 -5,115000001,120000001 -5,120000001,125000001 -5,125000001,130000001 -5,130000001,135000001 -5,135000001,140000001 -5,140000001,145000001 -5,145000001,150000001 -5,150000001,155000001 -5,155000001,160000001 -5,160000001,165000001 -5,165000001,170000001 -5,170000001,175000001 -5,175000001,180000001 -5,180000001,185000001 -6,1,5000001 -6,5000001,10000001 -6,10000001,15000001 -6,15000001,20000001 -6,20000001,25000001 -6,25000001,30000001 -6,30000001,35000001 -6,35000001,40000001 -6,40000001,45000001 -6,45000001,50000001 -6,50000001,55000001 -6,55000001,60000001 -6,60000001,65000001 -6,65000001,70000001 -6,70000001,75000001 -6,75000001,80000001 -6,80000001,85000001 -6,85000001,90000001 -6,90000001,95000001 -6,95000001,100000001 -6,100000001,105000001 -6,105000001,110000001 -6,110000001,115000001 -6,115000001,120000001 -6,120000001,125000001 -6,125000001,130000001 -6,130000001,135000001 -6,135000001,140000001 -6,140000001,145000001 -6,145000001,150000001 -6,150000001,155000001 -6,155000001,160000001 -6,160000001,165000001 -6,165000001,170000001 -6,170000001,175000001 -7,1,5000001 -7,5000001,10000001 -7,10000001,15000001 -7,15000001,20000001 -7,20000001,25000001 -7,25000001,30000001 -7,30000001,35000001 -7,35000001,40000001 -7,40000001,45000001 -7,45000001,50000001 -7,50000001,55000001 -7,55000001,60000001 -7,60000001,65000001 -7,65000001,70000001 -7,70000001,75000001 -7,75000001,80000001 -7,80000001,85000001 -7,85000001,90000001 -7,90000001,95000001 -7,95000001,100000001 -7,100000001,105000001 -7,105000001,110000001 -7,110000001,115000001 -7,115000001,120000001 -7,120000001,125000001 -7,125000001,130000001 -7,130000001,135000001 -7,135000001,140000001 -7,140000001,145000001 -7,145000001,150000001 -7,150000001,155000001 -7,155000001,160000001 -8,1,5000001 -8,5000001,10000001 -8,10000001,15000001 -8,15000001,20000001 -8,20000001,25000001 -8,25000001,30000001 -8,30000001,35000001 -8,35000001,40000001 -8,40000001,45000001 -8,45000001,50000001 -8,50000001,55000001 -8,55000001,60000001 -8,60000001,65000001 -8,65000001,70000001 -8,70000001,75000001 -8,75000001,80000001 -8,80000001,85000001 -8,85000001,90000001 -8,90000001,95000001 -8,95000001,100000001 -8,100000001,105000001 -8,105000001,110000001 -8,110000001,115000001 -8,115000001,120000001 -8,120000001,125000001 -8,125000001,130000001 -8,130000001,135000001 -8,135000001,140000001 -8,140000001,145000001 -8,145000001,150000001 -9,1,5000001 -9,5000001,10000001 -9,10000001,15000001 -9,15000001,20000001 -9,20000001,25000001 -9,25000001,30000001 -9,30000001,35000001 -9,35000001,40000001 -9,40000001,45000001 -9,45000001,50000001 -9,50000001,55000001 -9,55000001,60000001 -9,60000001,65000001 -9,65000001,70000001 -9,70000001,75000001 -9,75000001,80000001 -9,80000001,85000001 -9,85000001,90000001 -9,90000001,95000001 -9,95000001,100000001 -9,100000001,105000001 -9,105000001,110000001 -9,110000001,115000001 -9,115000001,120000001 -9,120000001,125000001 -9,125000001,130000001 -9,130000001,135000001 -9,135000001,140000001 -9,140000001,145000001 -10,1,5000001 -10,5000001,10000001 -10,10000001,15000001 -10,15000001,20000001 -10,20000001,25000001 -10,25000001,30000001 -10,30000001,35000001 -10,35000001,40000001 -10,40000001,45000001 -10,45000001,50000001 -10,50000001,55000001 -10,55000001,60000001 -10,60000001,65000001 -10,65000001,70000001 -10,70000001,75000001 -10,75000001,80000001 -10,80000001,85000001 -10,85000001,90000001 -10,90000001,95000001 -10,95000001,100000001 -10,100000001,105000001 -10,105000001,110000001 -10,110000001,115000001 -10,115000001,120000001 -10,120000001,125000001 -10,125000001,130000001 -10,130000001,135000001 -10,135000001,140000001 -11,1,5000001 -11,5000001,10000001 -11,10000001,15000001 -11,15000001,20000001 -11,20000001,25000001 -11,25000001,30000001 -11,30000001,35000001 -11,35000001,40000001 -11,40000001,45000001 -11,45000001,50000001 -11,50000001,55000001 -11,55000001,60000001 -11,60000001,65000001 -11,65000001,70000001 -11,70000001,75000001 -11,75000001,80000001 -11,80000001,85000001 -11,85000001,90000001 -11,90000001,95000001 -11,95000001,100000001 -11,100000001,105000001 -11,105000001,110000001 -11,110000001,115000001 -11,115000001,120000001 -11,120000001,125000001 -11,125000001,130000001 -11,130000001,135000001 -11,135000001,140000001 -12,1,5000001 -12,5000001,10000001 -12,10000001,15000001 -12,15000001,20000001 -12,20000001,25000001 -12,25000001,30000001 -12,30000001,35000001 -12,35000001,40000001 -12,40000001,45000001 -12,45000001,50000001 -12,50000001,55000001 -12,55000001,60000001 -12,60000001,65000001 -12,65000001,70000001 -12,70000001,75000001 -12,75000001,80000001 -12,80000001,85000001 -12,85000001,90000001 -12,90000001,95000001 -12,95000001,100000001 -12,100000001,105000001 -12,105000001,110000001 -12,110000001,115000001 -12,115000001,120000001 -12,120000001,125000001 -12,125000001,130000001 -12,130000001,135000001 -13,1,5000001 -13,5000001,10000001 -13,10000001,15000001 -13,15000001,20000001 -13,20000001,25000001 -13,25000001,30000001 -13,30000001,35000001 -13,35000001,40000001 -13,40000001,45000001 -13,45000001,50000001 -13,50000001,55000001 -13,55000001,60000001 -13,60000001,65000001 -13,65000001,70000001 -13,70000001,75000001 -13,75000001,80000001 -13,80000001,85000001 -13,85000001,90000001 -13,90000001,95000001 -13,95000001,100000001 -13,100000001,105000001 -13,105000001,110000001 -13,110000001,115000001 -13,115000001,120000001 -14,1,5000001 -14,5000001,10000001 -14,10000001,15000001 -14,15000001,20000001 -14,20000001,25000001 -14,25000001,30000001 -14,30000001,35000001 -14,35000001,40000001 -14,40000001,45000001 -14,45000001,50000001 -14,50000001,55000001 -14,55000001,60000001 -14,60000001,65000001 -14,65000001,70000001 -14,70000001,75000001 -14,75000001,80000001 -14,80000001,85000001 -14,85000001,90000001 -14,90000001,95000001 -14,95000001,100000001 -14,100000001,105000001 -14,105000001,110000001 -15,1,5000001 -15,5000001,10000001 -15,10000001,15000001 -15,15000001,20000001 -15,20000001,25000001 -15,25000001,30000001 -15,30000001,35000001 -15,35000001,40000001 -15,40000001,45000001 -15,45000001,50000001 -15,50000001,55000001 -15,55000001,60000001 -15,60000001,65000001 -15,65000001,70000001 -15,70000001,75000001 -15,75000001,80000001 -15,80000001,85000001 -15,85000001,90000001 -15,90000001,95000001 -15,95000001,100000001 -15,100000001,105000001 -16,1,5000001 -16,5000001,10000001 -16,10000001,15000001 -16,15000001,20000001 -16,20000001,25000001 -16,25000001,30000001 -16,30000001,35000001 -16,35000001,40000001 -16,40000001,45000001 -16,45000001,50000001 -16,50000001,55000001 -16,55000001,60000001 -16,60000001,65000001 -16,65000001,70000001 -16,70000001,75000001 -16,75000001,80000001 -16,80000001,85000001 -16,85000001,90000001 -16,90000001,95000001 -17,1,5000001 -17,5000001,10000001 -17,10000001,15000001 -17,15000001,20000001 -17,20000001,25000001 -17,25000001,30000001 -17,30000001,35000001 -17,35000001,40000001 -17,40000001,45000001 -17,45000001,50000001 -17,50000001,55000001 -17,55000001,60000001 -17,60000001,65000001 -17,65000001,70000001 -17,70000001,75000001 -17,75000001,80000001 -17,80000001,85000001 -18,1,5000001 -18,5000001,10000001 -18,10000001,15000001 -18,15000001,20000001 -18,20000001,25000001 -18,25000001,30000001 -18,30000001,35000001 -18,35000001,40000001 -18,40000001,45000001 -18,45000001,50000001 -18,50000001,55000001 -18,55000001,60000001 -18,60000001,65000001 -18,65000001,70000001 -18,70000001,75000001 -18,75000001,80000001 -19,1,5000001 -19,5000001,10000001 -19,10000001,15000001 -19,15000001,20000001 -19,20000001,25000001 -19,25000001,30000001 -19,30000001,35000001 -19,35000001,40000001 -19,40000001,45000001 -19,45000001,50000001 -19,50000001,55000001 -19,55000001,60000001 -20,1,5000001 -20,5000001,10000001 -20,10000001,15000001 -20,15000001,20000001 -20,20000001,25000001 -20,25000001,30000001 -20,30000001,35000001 -20,35000001,40000001 -20,40000001,45000001 -20,45000001,50000001 -20,50000001,55000001 -20,55000001,60000001 -20,60000001,65000001 -21,1,5000001 -21,5000001,10000001 -21,10000001,15000001 -21,15000001,20000001 -21,20000001,25000001 -21,25000001,30000001 -21,30000001,35000001 -21,35000001,40000001 -21,40000001,45000001 -21,45000001,50000001 -22,1,5000001 -22,5000001,10000001 -22,10000001,15000001 -22,15000001,20000001 -22,20000001,25000001 -22,25000001,30000001 -22,30000001,35000001 -22,35000001,40000001 -22,40000001,45000001 -22,45000001,50000001 -22,50000001,55000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr10Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr10Bins.csv deleted file mode 100644 index c7eaf755a2..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr10Bins.csv +++ /dev/null @@ -1,29 +0,0 @@ -chr,fromChrPos,toChrPos -10,1,5000001 -10,5000001,10000001 -10,10000001,15000001 -10,15000001,20000001 -10,20000001,25000001 -10,25000001,30000001 -10,30000001,35000001 -10,35000001,40000001 -10,40000001,45000001 -10,45000001,50000001 -10,50000001,55000001 -10,55000001,60000001 -10,60000001,65000001 -10,65000001,70000001 -10,70000001,75000001 -10,75000001,80000001 -10,80000001,85000001 -10,85000001,90000001 -10,90000001,95000001 -10,95000001,100000001 -10,100000001,105000001 -10,105000001,110000001 -10,110000001,115000001 -10,115000001,120000001 -10,120000001,125000001 -10,125000001,130000001 -10,130000001,135000001 -10,135000001,140000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr11Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr11Bins.csv deleted file mode 100644 index f7d3fa1361..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr11Bins.csv +++ /dev/null @@ -1,29 +0,0 @@ -chr,fromChrPos,toChrPos -11,1,5000001 -11,5000001,10000001 -11,10000001,15000001 -11,15000001,20000001 -11,20000001,25000001 -11,25000001,30000001 -11,30000001,35000001 -11,35000001,40000001 -11,40000001,45000001 -11,45000001,50000001 -11,50000001,55000001 -11,55000001,60000001 -11,60000001,65000001 -11,65000001,70000001 -11,70000001,75000001 -11,75000001,80000001 -11,80000001,85000001 -11,85000001,90000001 -11,90000001,95000001 -11,95000001,100000001 -11,100000001,105000001 -11,105000001,110000001 -11,110000001,115000001 -11,115000001,120000001 -11,120000001,125000001 -11,125000001,130000001 -11,130000001,135000001 -11,135000001,140000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr12Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr12Bins.csv deleted file mode 100644 index 034cd9ef35..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr12Bins.csv +++ /dev/null @@ -1,28 +0,0 @@ -chr,fromChrPos,toChrPos -12,1,5000001 -12,5000001,10000001 -12,10000001,15000001 -12,15000001,20000001 -12,20000001,25000001 -12,25000001,30000001 -12,30000001,35000001 -12,35000001,40000001 -12,40000001,45000001 -12,45000001,50000001 -12,50000001,55000001 -12,55000001,60000001 -12,60000001,65000001 -12,65000001,70000001 -12,70000001,75000001 -12,75000001,80000001 -12,80000001,85000001 -12,85000001,90000001 -12,90000001,95000001 -12,95000001,100000001 -12,100000001,105000001 -12,105000001,110000001 -12,110000001,115000001 -12,115000001,120000001 -12,120000001,125000001 -12,125000001,130000001 -12,130000001,135000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr13Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr13Bins.csv deleted file mode 100644 index dea912f7a4..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr13Bins.csv +++ /dev/null @@ -1,25 +0,0 @@ -chr,fromChrPos,toChrPos -13,1,5000001 -13,5000001,10000001 -13,10000001,15000001 -13,15000001,20000001 -13,20000001,25000001 -13,25000001,30000001 -13,30000001,35000001 -13,35000001,40000001 -13,40000001,45000001 -13,45000001,50000001 -13,50000001,55000001 -13,55000001,60000001 -13,60000001,65000001 -13,65000001,70000001 -13,70000001,75000001 -13,75000001,80000001 -13,80000001,85000001 -13,85000001,90000001 -13,90000001,95000001 -13,95000001,100000001 -13,100000001,105000001 -13,105000001,110000001 -13,110000001,115000001 -13,115000001,120000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr14Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr14Bins.csv deleted file mode 100644 index d2b4860bb4..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr14Bins.csv +++ /dev/null @@ -1,23 +0,0 @@ -chr,fromChrPos,toChrPos -14,1,5000001 -14,5000001,10000001 -14,10000001,15000001 -14,15000001,20000001 -14,20000001,25000001 -14,25000001,30000001 -14,30000001,35000001 -14,35000001,40000001 -14,40000001,45000001 -14,45000001,50000001 -14,50000001,55000001 -14,55000001,60000001 -14,60000001,65000001 -14,65000001,70000001 -14,70000001,75000001 -14,75000001,80000001 -14,80000001,85000001 -14,85000001,90000001 -14,90000001,95000001 -14,95000001,100000001 -14,100000001,105000001 -14,105000001,110000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr15Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr15Bins.csv deleted file mode 100644 index 90cef2dfe7..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr15Bins.csv +++ /dev/null @@ -1,22 +0,0 @@ -chr,fromChrPos,toChrPos -15,1,5000001 -15,5000001,10000001 -15,10000001,15000001 -15,15000001,20000001 -15,20000001,25000001 -15,25000001,30000001 -15,30000001,35000001 -15,35000001,40000001 -15,40000001,45000001 -15,45000001,50000001 -15,50000001,55000001 -15,55000001,60000001 -15,60000001,65000001 -15,65000001,70000001 -15,70000001,75000001 -15,75000001,80000001 -15,80000001,85000001 -15,85000001,90000001 -15,90000001,95000001 -15,95000001,100000001 -15,100000001,105000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr16Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr16Bins.csv deleted file mode 100644 index 5cd9c969a7..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr16Bins.csv +++ /dev/null @@ -1,20 +0,0 @@ -chr,fromChrPos,toChrPos -16,1,5000001 -16,5000001,10000001 -16,10000001,15000001 -16,15000001,20000001 -16,20000001,25000001 -16,25000001,30000001 -16,30000001,35000001 -16,35000001,40000001 -16,40000001,45000001 -16,45000001,50000001 -16,50000001,55000001 -16,55000001,60000001 -16,60000001,65000001 -16,65000001,70000001 -16,70000001,75000001 -16,75000001,80000001 -16,80000001,85000001 -16,85000001,90000001 -16,90000001,95000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr17Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr17Bins.csv deleted file mode 100644 index 0c986ff7b4..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr17Bins.csv +++ /dev/null @@ -1,18 +0,0 @@ -chr,fromChrPos,toChrPos -17,1,5000001 -17,5000001,10000001 -17,10000001,15000001 -17,15000001,20000001 -17,20000001,25000001 -17,25000001,30000001 -17,30000001,35000001 -17,35000001,40000001 -17,40000001,45000001 -17,45000001,50000001 -17,50000001,55000001 -17,55000001,60000001 -17,60000001,65000001 -17,65000001,70000001 -17,70000001,75000001 -17,75000001,80000001 -17,80000001,85000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr18Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr18Bins.csv deleted file mode 100644 index 428bdae2f8..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr18Bins.csv +++ /dev/null @@ -1,17 +0,0 @@ -chr,fromChrPos,toChrPos -18,1,5000001 -18,5000001,10000001 -18,10000001,15000001 -18,15000001,20000001 -18,20000001,25000001 -18,25000001,30000001 -18,30000001,35000001 -18,35000001,40000001 -18,40000001,45000001 -18,45000001,50000001 -18,50000001,55000001 -18,55000001,60000001 -18,60000001,65000001 -18,65000001,70000001 -18,70000001,75000001 -18,75000001,80000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr19Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr19Bins.csv deleted file mode 100644 index 9b20b0aadb..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr19Bins.csv +++ /dev/null @@ -1,13 +0,0 @@ -chr,fromChrPos,toChrPos -19,1,5000001 -19,5000001,10000001 -19,10000001,15000001 -19,15000001,20000001 -19,20000001,25000001 -19,25000001,30000001 -19,30000001,35000001 -19,35000001,40000001 -19,40000001,45000001 -19,45000001,50000001 -19,50000001,55000001 -19,55000001,60000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr1Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr1Bins.csv deleted file mode 100644 index c0277e6620..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr1Bins.csv +++ /dev/null @@ -1,51 +0,0 @@ -chr,fromChrPos,toChrPos -1,1,5000001 -1,5000001,10000001 -1,10000001,15000001 -1,15000001,20000001 -1,20000001,25000001 -1,25000001,30000001 -1,30000001,35000001 -1,35000001,40000001 -1,40000001,45000001 -1,45000001,50000001 -1,50000001,55000001 -1,55000001,60000001 -1,60000001,65000001 -1,65000001,70000001 -1,70000001,75000001 -1,75000001,80000001 -1,80000001,85000001 -1,85000001,90000001 -1,90000001,95000001 -1,95000001,100000001 -1,100000001,105000001 -1,105000001,110000001 -1,110000001,115000001 -1,115000001,120000001 -1,120000001,125000001 -1,125000001,130000001 -1,130000001,135000001 -1,135000001,140000001 -1,140000001,145000001 -1,145000001,150000001 -1,150000001,155000001 -1,155000001,160000001 -1,160000001,165000001 -1,165000001,170000001 -1,170000001,175000001 -1,175000001,180000001 -1,180000001,185000001 -1,185000001,190000001 -1,190000001,195000001 -1,195000001,200000001 -1,200000001,205000001 -1,205000001,210000001 -1,210000001,215000001 -1,215000001,220000001 -1,220000001,225000001 -1,225000001,230000001 -1,230000001,235000001 -1,235000001,240000001 -1,240000001,245000001 -1,245000001,250000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr20Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr20Bins.csv deleted file mode 100644 index e9e7dcdecc..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr20Bins.csv +++ /dev/null @@ -1,14 +0,0 @@ -chr,fromChrPos,toChrPos -20,1,5000001 -20,5000001,10000001 -20,10000001,15000001 -20,15000001,20000001 -20,20000001,25000001 -20,25000001,30000001 -20,30000001,35000001 -20,35000001,40000001 -20,40000001,45000001 -20,45000001,50000001 -20,50000001,55000001 -20,55000001,60000001 -20,60000001,65000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr21Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr21Bins.csv deleted file mode 100644 index 568f61a6b1..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr21Bins.csv +++ /dev/null @@ -1,11 +0,0 @@ -chr,fromChrPos,toChrPos -21,1,5000001 -21,5000001,10000001 -21,10000001,15000001 -21,15000001,20000001 -21,20000001,25000001 -21,25000001,30000001 -21,30000001,35000001 -21,35000001,40000001 -21,40000001,45000001 -21,45000001,50000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr22Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr22Bins.csv deleted file mode 100644 index a2a3362231..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr22Bins.csv +++ /dev/null @@ -1,12 +0,0 @@ -chr,fromChrPos,toChrPos -22,1,5000001 -22,5000001,10000001 -22,10000001,15000001 -22,15000001,20000001 -22,20000001,25000001 -22,25000001,30000001 -22,30000001,35000001 -22,35000001,40000001 -22,40000001,45000001 -22,45000001,50000001 -22,50000001,55000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr2Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr2Bins.csv deleted file mode 100644 index c6c00cf210..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr2Bins.csv +++ /dev/null @@ -1,50 +0,0 @@ -chr,fromChrPos,toChrPos -2,1,5000001 -2,5000001,10000001 -2,10000001,15000001 -2,15000001,20000001 -2,20000001,25000001 -2,25000001,30000001 -2,30000001,35000001 -2,35000001,40000001 -2,40000001,45000001 -2,45000001,50000001 -2,50000001,55000001 -2,55000001,60000001 -2,60000001,65000001 -2,65000001,70000001 -2,70000001,75000001 -2,75000001,80000001 -2,80000001,85000001 -2,85000001,90000001 -2,90000001,95000001 -2,95000001,100000001 -2,100000001,105000001 -2,105000001,110000001 -2,110000001,115000001 -2,115000001,120000001 -2,120000001,125000001 -2,125000001,130000001 -2,130000001,135000001 -2,135000001,140000001 -2,140000001,145000001 -2,145000001,150000001 -2,150000001,155000001 -2,155000001,160000001 -2,160000001,165000001 -2,165000001,170000001 -2,170000001,175000001 -2,175000001,180000001 -2,180000001,185000001 -2,185000001,190000001 -2,190000001,195000001 -2,195000001,200000001 -2,200000001,205000001 -2,205000001,210000001 -2,210000001,215000001 -2,215000001,220000001 -2,220000001,225000001 -2,225000001,230000001 -2,230000001,235000001 -2,235000001,240000001 -2,240000001,245000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr3Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr3Bins.csv deleted file mode 100644 index eb999fb559..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr3Bins.csv +++ /dev/null @@ -1,41 +0,0 @@ -chr,fromChrPos,toChrPos -3,1,5000001 -3,5000001,10000001 -3,10000001,15000001 -3,15000001,20000001 -3,20000001,25000001 -3,25000001,30000001 -3,30000001,35000001 -3,35000001,40000001 -3,40000001,45000001 -3,45000001,50000001 -3,50000001,55000001 -3,55000001,60000001 -3,60000001,65000001 -3,65000001,70000001 -3,70000001,75000001 -3,75000001,80000001 -3,80000001,85000001 -3,85000001,90000001 -3,90000001,95000001 -3,95000001,100000001 -3,100000001,105000001 -3,105000001,110000001 -3,110000001,115000001 -3,115000001,120000001 -3,120000001,125000001 -3,125000001,130000001 -3,130000001,135000001 -3,135000001,140000001 -3,140000001,145000001 -3,145000001,150000001 -3,150000001,155000001 -3,155000001,160000001 -3,160000001,165000001 -3,165000001,170000001 -3,170000001,175000001 -3,175000001,180000001 -3,180000001,185000001 -3,185000001,190000001 -3,190000001,195000001 -3,195000001,200000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr4Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr4Bins.csv deleted file mode 100644 index 5bf44c6850..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr4Bins.csv +++ /dev/null @@ -1,40 +0,0 @@ -chr,fromChrPos,toChrPos -4,1,5000001 -4,5000001,10000001 -4,10000001,15000001 -4,15000001,20000001 -4,20000001,25000001 -4,25000001,30000001 -4,30000001,35000001 -4,35000001,40000001 -4,40000001,45000001 -4,45000001,50000001 -4,50000001,55000001 -4,55000001,60000001 -4,60000001,65000001 -4,65000001,70000001 -4,70000001,75000001 -4,75000001,80000001 -4,80000001,85000001 -4,85000001,90000001 -4,90000001,95000001 -4,95000001,100000001 -4,100000001,105000001 -4,105000001,110000001 -4,110000001,115000001 -4,115000001,120000001 -4,120000001,125000001 -4,125000001,130000001 -4,130000001,135000001 -4,135000001,140000001 -4,140000001,145000001 -4,145000001,150000001 -4,150000001,155000001 -4,155000001,160000001 -4,160000001,165000001 -4,165000001,170000001 -4,170000001,175000001 -4,175000001,180000001 -4,180000001,185000001 -4,185000001,190000001 -4,190000001,195000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr5Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr5Bins.csv deleted file mode 100644 index b1a12c4877..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr5Bins.csv +++ /dev/null @@ -1,38 +0,0 @@ -chr,fromChrPos,toChrPos -5,1,5000001 -5,5000001,10000001 -5,10000001,15000001 -5,15000001,20000001 -5,20000001,25000001 -5,25000001,30000001 -5,30000001,35000001 -5,35000001,40000001 -5,40000001,45000001 -5,45000001,50000001 -5,50000001,55000001 -5,55000001,60000001 -5,60000001,65000001 -5,65000001,70000001 -5,70000001,75000001 -5,75000001,80000001 -5,80000001,85000001 -5,85000001,90000001 -5,90000001,95000001 -5,95000001,100000001 -5,100000001,105000001 -5,105000001,110000001 -5,110000001,115000001 -5,115000001,120000001 -5,120000001,125000001 -5,125000001,130000001 -5,130000001,135000001 -5,135000001,140000001 -5,140000001,145000001 -5,145000001,150000001 -5,150000001,155000001 -5,155000001,160000001 -5,160000001,165000001 -5,165000001,170000001 -5,170000001,175000001 -5,175000001,180000001 -5,180000001,185000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr6Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr6Bins.csv deleted file mode 100644 index 4b5cf9509e..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr6Bins.csv +++ /dev/null @@ -1,36 +0,0 @@ -chr,fromChrPos,toChrPos -6,1,5000001 -6,5000001,10000001 -6,10000001,15000001 -6,15000001,20000001 -6,20000001,25000001 -6,25000001,30000001 -6,30000001,35000001 -6,35000001,40000001 -6,40000001,45000001 -6,45000001,50000001 -6,50000001,55000001 -6,55000001,60000001 -6,60000001,65000001 -6,65000001,70000001 -6,70000001,75000001 -6,75000001,80000001 -6,80000001,85000001 -6,85000001,90000001 -6,90000001,95000001 -6,95000001,100000001 -6,100000001,105000001 -6,105000001,110000001 -6,110000001,115000001 -6,115000001,120000001 -6,120000001,125000001 -6,125000001,130000001 -6,130000001,135000001 -6,135000001,140000001 -6,140000001,145000001 -6,145000001,150000001 -6,150000001,155000001 -6,155000001,160000001 -6,160000001,165000001 -6,165000001,170000001 -6,170000001,175000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr7Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr7Bins.csv deleted file mode 100644 index cb8f770633..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr7Bins.csv +++ /dev/null @@ -1,33 +0,0 @@ -chr,fromChrPos,toChrPos -7,1,5000001 -7,5000001,10000001 -7,10000001,15000001 -7,15000001,20000001 -7,20000001,25000001 -7,25000001,30000001 -7,30000001,35000001 -7,35000001,40000001 -7,40000001,45000001 -7,45000001,50000001 -7,50000001,55000001 -7,55000001,60000001 -7,60000001,65000001 -7,65000001,70000001 -7,70000001,75000001 -7,75000001,80000001 -7,80000001,85000001 -7,85000001,90000001 -7,90000001,95000001 -7,95000001,100000001 -7,100000001,105000001 -7,105000001,110000001 -7,110000001,115000001 -7,115000001,120000001 -7,120000001,125000001 -7,125000001,130000001 -7,130000001,135000001 -7,135000001,140000001 -7,140000001,145000001 -7,145000001,150000001 -7,150000001,155000001 -7,155000001,160000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr8Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr8Bins.csv deleted file mode 100644 index 121c665561..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr8Bins.csv +++ /dev/null @@ -1,31 +0,0 @@ -chr,fromChrPos,toChrPos -8,1,5000001 -8,5000001,10000001 -8,10000001,15000001 -8,15000001,20000001 -8,20000001,25000001 -8,25000001,30000001 -8,30000001,35000001 -8,35000001,40000001 -8,40000001,45000001 -8,45000001,50000001 -8,50000001,55000001 -8,55000001,60000001 -8,60000001,65000001 -8,65000001,70000001 -8,70000001,75000001 -8,75000001,80000001 -8,80000001,85000001 -8,85000001,90000001 -8,90000001,95000001 -8,95000001,100000001 -8,100000001,105000001 -8,105000001,110000001 -8,110000001,115000001 -8,115000001,120000001 -8,120000001,125000001 -8,125000001,130000001 -8,130000001,135000001 -8,135000001,140000001 -8,140000001,145000001 -8,145000001,150000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr9Bins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr9Bins.csv deleted file mode 100644 index 0bded93059..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/b37Chr9Bins.csv +++ /dev/null @@ -1,30 +0,0 @@ -chr,fromChrPos,toChrPos -9,1,5000001 -9,5000001,10000001 -9,10000001,15000001 -9,15000001,20000001 -9,20000001,25000001 -9,25000001,30000001 -9,30000001,35000001 -9,35000001,40000001 -9,40000001,45000001 -9,45000001,50000001 -9,50000001,55000001 -9,55000001,60000001 -9,60000001,65000001 -9,65000001,70000001 -9,70000001,75000001 -9,75000001,80000001 -9,80000001,85000001 -9,85000001,90000001 -9,90000001,95000001 -9,95000001,100000001 -9,100000001,105000001 -9,105000001,110000001 -9,110000001,115000001 -9,115000001,120000001 -9,120000001,125000001 -9,125000001,130000001 -9,130000001,135000001 -9,135000001,140000001 -9,140000001,145000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/testbuild37ChrBins.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/testbuild37ChrBins.csv deleted file mode 100644 index 7f267a2feb..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/ChrBins/testbuild37ChrBins.csv +++ /dev/null @@ -1,14 +0,0 @@ -chr,fromChrPos,toChrPos -20,1,5000001 -20,5000001,10000001 -20,10000001,15000001 -20,15000001,20000001 -20,20000001,25000001 -20,25000001,30000001 -20,30000001,35000001 -20,35000001,40000001 -20,40000001,45000001 -20,45000001,50000001 -20,50000001,55000001 -20,55000001,60000001 -20,60000001,65000001 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/README.md b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/README.md deleted file mode 100644 index 8f38ece1db..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/README.md +++ /dev/null @@ -1,194 +0,0 @@ -Imputation using Molgenis Compute -============================ - -Blaat blaat blaat etc. - -Content -======= - -1. Introduction -2. Running compute -3. Worksheet -4. Parameters -5. Protocols -6. Workflows -7. Imputation - - -Introduction -============ - -Parameters -========== - -Worksheet -========= - -Folding the worksheet ---------------------- - -[sec:folding] É - -Protocol -======== - -A protocol is a template in the Freemarker[^1] language that describes -the work to be done. A protocol may therefore contain one or more -parameters, like `${myFile}`, that are specified in your parameter list -or worksheet. A protocol consists of the following four parts as -explained below. - -Header ------- - -The header of a protocol may contain the following line in which you -specify the hardware requirements for your analysis. - -`#MOLGENIS walltime=hh:mm:ss mem=m nodes=n cores=c` - -where walltime is the maximum execution time, $m$ is the memory (*e.g.* -512MB or 4GB), $n$ is the number of nodes and $c$ is the number of cores -that you request for the execution of this analysis. - -Usually, a protocol is be applied to every row in the worksheet. -However, some protocols may apply to specific targets (*i.e.* parameters -that are specified in the worksheet); see Section [sec:folding] for more -detail. The targets (say $target1$ and $target2$) are specified with the -following statement. - -`#FOREACH target1, target2` - -Download your data ------------------- - -A protocol may be executed in a distributed environment. As a result, -the data may not be available where the execution takes place. -Therefore, one should first download the data to the execution node. For -every file that you want to use in the analysis protocol, you need to -include the following statement in the protocol before using it. - -`getFile "$myInputFile"` - -Where `"myInputFile"` is a parameter in your parameter list that refers -to the file. If this file is an executable, you may want to make it -executable by adding the following statement to your protocol. - -`chmod +x "$myInputFile"` - -Analysis template ------------------ - -After downloading the data you can specify the analysis you want to run. - -Upload your data ----------------- - -After finishing the analysis, you may save the files you want to keep by -including the following statement at the end of your protocol. - -`putFile "$myOutputFile"` - -Where `"myOutputFile"` again is a parameter in your parameter list that -refers to the respective file. - -Workflow -======== - - - -Imputation -========== - -All imputation protocols are stored in the *protocols/imputation/* directory. This -directory contains multiple sub-directories: - -* beagle -* impute2 -* mach_minimach -* prepareReference - -Each of these directories contain the following files to be used as input for Molgenis -Compute: - -* parameters.csv -* workflow.csv -* worksheet.csv -* protocols (*.ftl files) - - -Preparing the reference dataset -------------------------------- - - -To start imputation on a cohort one first has to prepare the reference data. The -*prepareReference* directory contains several protocols to prepare this data. - -###Generating a reference data set -This workflow requires a VCF file containing phased genotypes as input. The workflow requires the VCF files to be split per chromosome in a folder named *vcf*. When executing this workflow two folders containing the data in Impute2 and TriTyper format per chromosome are generated. - - -An example test reference set can be created using the following command: ->sh molgenis_compute.sh \\ ->*-*worksheet=protocols/imputation/prepareReference/prepareReferenceWorksheetSample.csv \\ ->*-*parameters=protocols/imputation/prepareReference/parameters.csv \\ ->*-*workflow=protocols/imputation/prepareReference/prepareReferenceWorkflow.csv \\ ->*-*protocols=protocols/imputation/prepareReference/ \\ ->*-*templates=protocols/imputation/prepareReference/ \\ ->*-*scripts=/your/output/directory/here/ \\ ->*-*id=runXX - -###Output example -Executing the above mentioned command will result in a directory with the following structure: - - - - -referenceName - -Impute2 - chrNumber.impute.hap - chrNumber.impute.hap.indv - chrNumber.impute.legend - -TriTyper - -ChrchrNumber - GenotypeMatrix.dat - Individuals.txt - PhenotypeInformation.txt - SNPMappings.txt - SNPs.txt - -vcf - chrNumber.vcf - chrNumber.vcf.vcfidx - - Note: - - The vcf directory contains the input VCF files split per chromosome. The *.vcf.vcfidx file is generated in this workflow. - - Genetic recombination maps for each chromosome should be added to the Impute2 directory manually. - Afterwards the filename convention should be specified in the parameters.csv file of the impute2 workflow. - - -**HOW CAN NOTE 2 BE EXPLAINED BETTER?** - -When all these files are present the reference dataset is ready to be used. - - -Imputation using Impute2 ------------------------- - - -All protocols and files to run an imputation using Impute2 can be found in the *protocols/imputation/impute2/* directory. - - - - - - -Imputation using Beagle ------------------------ - - - -Imputation using Mach ---------------------- - - - - -[^1]: See http://freemarker.org/ for a manual. diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/createDir.sh b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/createDir.sh deleted file mode 100644 index 4d06e64dfc..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/createDir.sh +++ /dev/null @@ -1,83 +0,0 @@ -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools/ImputationTool-20120912 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools/ImputationTool-20120912/lib -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/liftover -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/Impute2 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper/Chr20 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/eQtl -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/eQtl/hapmap2r24ceu -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/b36PedMap -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/ -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/b36conversion -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/Impute2Result -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/Impute2Result/20 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/preparedStudy -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/preparedStudy/20 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/StudyTriTyper -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/StudyTriTyper/chr20 -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/PedMap -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/imputationResult/hapmap2r24ceu_Impute2_refGoNL_allChrs/tmp/PedMap/chr20 - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/Impute2/20.impute.hap \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/Impute2/20.impute.hap - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/Impute2/20.impute.hap.indv \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/Impute2/20.impute.hap.indv - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/Impute2/20.impute.legend \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/Impute2/20.impute.legend - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/Impute2/genetic_map_chr20_combined_b37.txt \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/Impute2/genetic_map_chr20_combined_b37.txt - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/TriTyper/Chr20/GenotypeMatrix.dat \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper/Chr20/GenotypeMatrix.dat - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/TriTyper/Chr20/Individuals.txt \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper/Chr20/Individuals.txt - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/TriTyper/Chr20/PhenotypeInformation.txt \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper/Chr20/PhenotypeInformation.txt - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/TriTyper/Chr20/SNPMappings.txt \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper/Chr20/SNPMappings.txt - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/gonl_release3.1/TriTyper/Chr20/SNPs.txt \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/imputationReference/gonl_release3.1/TriTyper/Chr20/SNPs.txt - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/hapmap2r24ceu/chr20.map \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/eQtl/hapmap2r24ceu/chr20.map - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/hapmap2r24ceu/chr20.ped \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/groups/gonl/projects/imputationBenchmarking/eQtl/hapmap2r24ceu/chr20.ped - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/resources/liftover/hg18ToHg19.over.chain \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/liftover/hg18ToHg19.over.chain - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/resources/liftover/hg19ToHg18.over.chain \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/resources/liftover/hg19ToHg18.over.chain - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/tools/ImputationTool-20120912/lib/GeneticaLibraries.jar \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools/ImputationTool-20120912/lib/GeneticaLibraries.jar - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/tools/ImputationTool-20120912/lib/jsci-core-1.1.jar \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools/ImputationTool-20120912/lib/jsci-core-1.1.jar - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/tools/ImputationTool-20120912/ImputationTool.jar \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools/ImputationTool-20120912/ImputationTool.jar - -srmmkdir srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools//python_scripts - -srmcp -server_mode=passive file:///$HOME/impute2-test-run/tools/python_scripts/calculateBeagleR2ForImpute2Results.py \ -srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/byelas/tools/python_scripts/calculateBeagleR2ForImpute2Results.py \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/createWorkflowImpute.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/createWorkflowImpute.csv deleted file mode 100644 index 0cce1a9a0f..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/createWorkflowImpute.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -createImputationScriptsAndWorksheet,createImputationScriptsAndWorksheet, \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/parameters.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/parameters.csv deleted file mode 100644 index 3a07b3e60c..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/parameters.csv +++ /dev/null @@ -1,86 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,gcc,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,GRID,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,$WORKDIR,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -resdir,${root}/resources,,, -#,,,, -tempdir,${imputationResultDir}/tmp/,,, -plink,${tooldir}/plink-${plinkversion}/plink,,, -plinkversion,1.07-x86_64,,, -plinkseqBin,${tooldir}/plink-${plinkseqversion}/plink108,,, -plinkseqversion,1.08,,, -projectComputeDir,${imputationResultDir}/compute,,, -projectJobsDir,${projectComputeDir}/jobs,,, -projectChrJobsDir,${projectJobsDir}/chr${chr},,, -projectTempDir,${tempdir}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyInputPedMapChr,${studyInputDir}/chr${chr},,, -studyPedMapChrDir,${studyPedMapDir}/chr${chr}/,,, -studyPedMapChr,${studyPedMapChrDir}/chr${chr},,, -studyTriTyperChrTempDir,${projectTempDir}/StudyTriTyper/~chr${chr}/,end with slash,, -studyTriTyperChrDir,${projectTempDir}/StudyTriTyper/chr${chr}/,end with slash,, -preparedStudyTempDir,${projectTempDir}/preparedStudy/~${chr}/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/${chr}/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -chrBinsDir,${McProtocols}/ChrBins/,,, -allChrBinsFile,${chrBinsDir}/b37AllChrBins.csv,,, -chrBinsFile,${chrBinsDir}/b37Chr${chr}Bins.csv,,, -gtoolBin,gtool,,, -#gtoolBin,${tooldir}/gtool_${gtoolBinversion}/gtool,,, -gtoolBinversion,v0.7.5_x86_64,,, -referenceFolder,${resdir}/imputationReference/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/Chr${chr}/,end with slash,, -referenceImpute2Dir,${referenceFolder}/${referencePanel}/Impute2/,end with slash,, -pythonversion,2.7.3,,, -javaversion,1.6.0_33,,, -impute,impute,,, -impute2Bin,impute2,,, -#impute2Bin,${tooldir}/impute_${impute2Binversion}/impute2,,, -impute2Binversion,v2.2.2_x86_64_static,,, -imputationToolJar,${tooldir}/ImputationTool-${imputationToolJarversion}/ImputationTool.jar,,, -imputationToolJarversion,20120912,,, -imputationToolLibDir,${tooldir}/ImputationTool-${imputationToolJarversion}/lib/,,, -imputationToolGeneticaLibrariesJar,${imputationToolLibDir}/GeneticaLibraries.jar,,, -imputationToolJsciCoreJar,${imputationToolLibDir}/jsci-core-1.1.jar,,, -referenceImpute2HapFile,${referenceImpute2Dir}/${chr}.impute.hap,,, -referenceImpute2LegendFile,${referenceImpute2Dir}/${chr}.impute.legend,,, -referenceImpute2MapFile,${referenceImpute2Dir}/genetic_map_chr${chr}_combined_${genomeBuild}.txt,,, -impute2ResultDir,${projectTempDir}/Impute2Result/,end with slash,, -calculateBeagleR2ForIMpute2ResultsPythonScript,${tooldir}/python_scripts/calculateBeagleR2ForImpute2Results.py,,, -impute2ResultChrBinTemp,${impute2ResultDir}/${chr}/~chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBin,${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBinLog,${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}.log,,, -impute2ResultChrBinGenFile,${impute2ResultChrBin},,, -impute2ResultChrBinInfoFile,${impute2ResultChrBin}_info,,, -convertB36ChrTempDir,${projectTempDir}/b36conversion/,,, -convertB36ChrHg19Bed,${convertB36ChrTempDir}/chr_${chr}Hg19.bed,,, -convertB36unmapped,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -convertB36unmappedSNPs,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -b36conversionPedMapResultDir,${imputationResultDir}/b36PedMap/,,, -liftOverUcscBin,${tooldir}/liftOverUcsc-${liftOverUcscBinversion}/liftOver,,, -liftOverUcscBinversion,20120905,,, -convertB36ChrHg18Bed,${convertB36ChrTempDir}/chr_${chr}Hg18.bed,,, -liftoverDir,${resdir}/liftover/,,, -hg19ToHg18chainfile,${liftoverDir}/hg19ToHg18.over.chain,,, -project,,,,"imputationResultDir,studyInputDir,referencePanel,imputationPipeline" -expandWorksheetJar,${tooldir}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}.jar,,, -expandWorksheetJarversion,V1.0,,, -#,,,, -chr,,,, -toChrPos,,Temp variable which will be overwritten with value in worksheet,, -fromChrPos,,Temp variable which will be overwritten with value in worksheet,, -#,,,, -studyInputDir,,,, -referencePanel,,,, -imputationResultDir,,,, -imputationPipeline,,,, -genomeBuild,,,, diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index f751574c46..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,12 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - - -#For SGE -#-hold_jid \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Footer.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Header.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Header.ftl deleted file mode 100644 index d6f70bbef6..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Header.ftl +++ /dev/null @@ -1,34 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#$ -S /bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - -<#elseif scheduler == "GRID"> - - - - -<#if scheduler != "GRID"> -# Configures the GCC bash environment -. ${root}/gcc.bashrc - - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Helpers.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Macros.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/NGSHeader.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/calculateBeagleR2ForImpute2Results.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/calculateBeagleR2ForImpute2Results.ftl deleted file mode 100644 index c6ad2c223e..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/calculateBeagleR2ForImpute2Results.ftl +++ /dev/null @@ -1,15 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${calculateBeagleR2ForIMpute2ResultsPythonScript} -getFile ${imputationResultDir}/chr_${chr} - -inputs "${imputationResultDir}/chr_${chr}" -alloutputsexist "${imputationResultDir}/chr_${chr}.beagleR2" - -module load Python/${pythonversion} - -python ${calculateBeagleR2ForIMpute2ResultsPythonScript} ${imputationResultDir}/chr_${chr} ${imputationResultDir}/chr_${chr}.beagleR2 - -putFile ${imputationResultDir}/chr_${chr}.beagleR2 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/concatImpute2ResultsPerChr.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/concatImpute2ResultsPerChr.ftl deleted file mode 100644 index 4284485b85..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/concatImpute2ResultsPerChr.ftl +++ /dev/null @@ -1,26 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -<#list impute2ResultChrBinInfoFile as infoFile> - getFile ${infoFile} - -<#list impute2ResultChrBinGenFile as genFile> - getFile ${genFile} - - - - -inputs "${ssvQuoted(impute2ResultChrBinInfoFile)}" -inputs "${ssvQuoted(impute2ResultChrBinGenFile)}" -alloutputsexist "${imputationResultDir}/chr_${chr}" \ -"${imputationResultDir}/chr_${chr}_info" - -#Concat the bins with compute for each - -cat ${ssvQuoted(impute2ResultChrBinInfoFile)} > ${imputationResultDir}/chr_${chr}_info - -cat ${ssvQuoted(impute2ResultChrBinGenFile)} > ${imputationResultDir}/chr_${chr} - -putFile ${imputationResultDir}/chr_${chr} -putFile ${imputationResultDir}/chr_${chr}_info diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertConcatedImpute2ResultToPedMap.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertConcatedImpute2ResultToPedMap.ftl deleted file mode 100644 index dec35da34a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertConcatedImpute2ResultToPedMap.ftl +++ /dev/null @@ -1,47 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${imputationResultDir}/chr_${chr} -getFile ${preparedStudyDir}/chr${chr}.sample - -inputs "${imputationResultDir}/chr_${chr}" -inputs "${preparedStudyDir}/chr${chr}.sample" -alloutputsexist "${imputationResultDir}/chr_${chr}.ped" \ -"${imputationResultDir}/chr_${chr}.map" - - -module load ${gtoolBin}/${gtoolBinversion} - -${gtoolBin} \ --G \ ---g ${imputationResultDir}/chr_${chr} \ ---s ${preparedStudyDir}/chr${chr}.sample \ ---ped ${imputationResultDir}/~chr_${chr}.ped \ ---map ${imputationResultDir}/~chr_${chr}.map \ ---snp \ ---chr ${chr} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${imputationResultDir}/~chr_${chr}.ped ${imputationResultDir}/chr_${chr}.ped - mv ${imputationResultDir}/~chr_${chr}.map ${imputationResultDir}/chr_${chr}.map - - putFile ${imputationResultDir}/chr_${chr}.ped - putFile ${imputationResultDir}/chr_${chr}.map - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertPedMapToTriTyper.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertPedMapToTriTyper.ftl deleted file mode 100644 index e92cc5266d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertPedMapToTriTyper.ftl +++ /dev/null @@ -1,61 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile "${imputationToolJar}" -getFile "${imputationToolJsciCoreJar}" -getFile "${imputationToolGeneticaLibrariesJar}" - -getFile "${studyPedMapChr}.map" -getFile "${studyPedMapChr}.ped" - - - -inputs "${studyPedMapChr}.map" -inputs "${studyPedMapChr}.ped" -alloutputsexist "${studyTriTyperChrDir}/GenotypeMatrix.dat" \ -"${studyTriTyperChrDir}/Individuals.txt" \ -"${studyTriTyperChrDir}/PhenotypeInformation.txt" \ -"${studyTriTyperChrDir}/SNPMappings.txt" \ -"${studyTriTyperChrDir}/SNPs.txt" - - -if [ -d ${studyTriTyperChrDir} ] -then - rm -r ${studyTriTyperChrDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${studyTriTyperChrTempDir} - -java -jar ${imputationToolJar} \ ---mode pmtt \ ---in ${studyPedMapChrDir} \ ---out ${studyTriTyperChrTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${studyTriTyperChrTempDir} ${studyTriTyperChrDir} - - putFile "${studyTriTyperChrDir}/GenotypeMatrix.dat" - putFile "${studyTriTyperChrDir}/Individuals.txt" - putFile "${studyTriTyperChrDir}/PhenotypeInformation.txt" - putFile "${studyTriTyperChrDir}/SNPMappings.txt" - putFile "${studyTriTyperChrDir}/SNPs.txt" - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertPreparedStudyPedMapToGen.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertPreparedStudyPedMapToGen.ftl deleted file mode 100644 index 815904ae72..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertPreparedStudyPedMapToGen.ftl +++ /dev/null @@ -1,50 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${preparedStudyDir}/chr${chr}.ped -getFile ${preparedStudyDir}/chr${chr}.map -getFile ${studyPedMapChr}.ped - -inputs "${preparedStudyDir}/chr${chr}.ped" -inputs "${preparedStudyDir}/chr${chr}.map" -inputs "${studyPedMapChr}.ped" -alloutputsexist "${preparedStudyDir}/chr${chr}.gen" \ -"${preparedStudyDir}/chr${chr}.sample" - - -module load ${gtoolBin}/${gtoolBinversion} - -${gtoolBin} -P \ ---ped ${preparedStudyDir}/chr${chr}.ped \ ---map ${preparedStudyDir}/chr${chr}.map \ ---og ${preparedStudyDir}/~chr${chr}.gen - -awk ' - BEGIN { print "ID_1 ID_2 missing sex phenotype"; print "0 0 0 D P"} - {print $2,$1,"0",$5,$6} -' OFS=" " ${studyPedMapChr}.ped \ -> ${preparedStudyDir}/~chr${chr}.sample - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${preparedStudyDir}/~chr${chr}.gen ${preparedStudyDir}/chr${chr}.gen - mv ${preparedStudyDir}/~chr${chr}.sample ${preparedStudyDir}/chr${chr}.sample - - putFile ${preparedStudyDir}/chr${chr}.gen - putFile ${preparedStudyDir}/chr${chr}.sample - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertResultPedMapToB36.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertResultPedMapToB36.ftl deleted file mode 100644 index eb790c7e3a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertResultPedMapToB36.ftl +++ /dev/null @@ -1,64 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${imputationResultDir}/chr_${chr}.map -getFile ${hg19ToHg18chainfile} -getFile ${imputationResultDir}/chr_${chr}.ped - - -inputs "${imputationResultDir}/chr_${chr}.map" -inputs "${hg19ToHg18chainfile}" -inputs "${imputationResultDir}/chr_${chr}.ped" -alloutputsexist "${convertB36ChrHg19Bed}" \ -"${convertB36ChrHg18Bed}" \ -"${convertB36unmapped}" \ -"${b36conversionPedMapResultDir}/chr_${chr}.map" \ -"${b36conversionPedMapResultDir}/chr_${chr}.ped" \ -"${convertB36unmappedSNPs}" - -#module load ${liftOverUcscBin}/${liftOverUcscBinversion} -#module load ${plinkseqBin}/${plinkseqversion} - -mkdir -p ${convertB36ChrTempDir} - -#Create hg19 bed file from map file -awk '{$5=$2;$2=$4;$3=$4+1;$1="chr"$1;print $1,$2,$3,$5}' OFS="\t" ${imputationResultDir}/chr_${chr}.map \ -> ${convertB36ChrHg19Bed} - -#Lift over hg19 bed to hg18 bed -${liftOverUcscBin} \ --bedPlus=4 \ -${convertB36ChrHg19Bed} \ -${hg19ToHg18chainfile} \ -${convertB36ChrHg18Bed} \ -${convertB36unmapped} - -#Select SNP ID from non-lifted over SNPs -awk '/^[^#]/ {print $4}' \ -${convertB36unmapped} \ -> ${convertB36unmappedSNPs} - -mkdir -p ${b36conversionPedMapResultDir} - -#Generate new Ped/Map file excluding SNPs which were NOT lifted over -${plinkseqBin} \ ---noweb \ ---recode \ ---ped ${imputationResultDir}/chr_${chr}.ped \ ---map ${imputationResultDir}/chr_${chr}.map \ ---out ${b36conversionPedMapResultDir}/chr_${chr} \ ---exclude ${convertB36unmappedSNPs} \ ---missing-genotype N - -#Create new map file from hg18 bed -awk '{sub("chr","",$1);print $1,$4,0,$2}' OFS="\t" \ -${convertB36ChrHg18Bed} \ -> ${b36conversionPedMapResultDir}/chr_${chr}.map - -putFile ${convertB36ChrHg19Bed} -putFile ${convertB36ChrHg18Bed} -putFile ${convertB36unmapped} -putFile ${b36conversionPedMapResultDir}/chr_${chr}.map -putFile ${b36conversionPedMapResultDir}/chr_${chr}.ped -putFile ${convertB36unmappedSNPs} diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertResultPedMapToVcf.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertResultPedMapToVcf.ftl deleted file mode 100644 index 91a7fa3472..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/convertResultPedMapToVcf.ftl +++ /dev/null @@ -1,42 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${imputationResultDir}/chr_${chr}.ped -getFile ${imputationResultDir}/chr_${chr}.map - -inputs "${imputationResultDir}/chr_${chr}.ped" -inputs "${imputationResultDir}/chr_${chr}.map" -alloutputsexist "${imputationResultDir}/chr_${chr}.vcf" - - -#module load ${plinkseqBin}/${plinkseqversion} - - -${plinkseqBin} \ ---noweb \ ---recode-vcf \ ---ped ${imputationResultDir}/chr_${chr}.ped \ ---map ${imputationResultDir}/chr_${chr}.map \ ---out ${imputationResultDir}/~chr_${chr} \ ---missing-genotype N - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${imputationResultDir}/~chr_${chr}.vcf ${imputationResultDir}/chr_${chr}.vcf - - putFile ${imputationResultDir}/chr_${chr}.vcf - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/createImputationScriptsAndWorksheet.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/createImputationScriptsAndWorksheet.ftl deleted file mode 100644 index 4bf76e7708..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/createImputationScriptsAndWorksheet.ftl +++ /dev/null @@ -1,43 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project - -getFile ${expandWorksheetJar} - -getFile ${McWorksheet} -getFile ${chrBinsFile} -#putFile ${projectComputeDir}/${project}.worksheet.csv - -inputs "${McWorksheet}" -inputs "${chrBinsFile}" -#alloutputsexist "${expandedWorksheet}" - - -mkdir -p ${projectTempDir} -mkdir -p ${projectJobsDir} - -module load jdk/${javaversion} - -#Run Jar to create full worksheet - -<#if imputationPipeline == "impute2"> - - - java -jar ${expandWorksheetJar} ${McWorksheet} ${expandedWorksheet} ${chrBinsFile} project ${project} - - # Execute MOLGENIS/compute to create job scripts. - sh ${McDir}/molgenis_compute.sh \ - -worksheet=${expandedWorksheet} \ - -parameters=${McParameters} \ - -workflow=${McProtocols}/workflowImpute.csv \ - -protocols=${McProtocols}/ \ - -templates=${McTemplates}/ \ - -scripts=${projectJobsDir}/ \ - -id=${McId} - -<#else> - - echo "imputationPipeline ${imputationPipeline} not supported" - return 1 - - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/imputeWithImpute2.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/imputeWithImpute2.ftl deleted file mode 100644 index 6d4a0312ba..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/imputeWithImpute2.ftl +++ /dev/null @@ -1,78 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - - - -getFile ${referenceImpute2HapFile} -getFile ${referenceImpute2LegendFile} -getFile ${referenceImpute2MapFile} -getFile ${preparedStudyDir}/chr${chr}.gen - -inputs "${referenceImpute2HapFile}" -inputs "${referenceImpute2LegendFile}" -inputs "${referenceImpute2MapFile}" -inputs "${preparedStudyDir}/chr${chr}.gen" -alloutputsexist "${impute2ResultChrBin}" \ -"${impute2ResultChrBin}_info" \ -"${impute2ResultChrBin}_info_by_sample" \ -"${impute2ResultChrBin}_summary" \ -"${impute2ResultChrBin}_warnings" - - -module load ${impute}/${impute2Binversion} - -mkdir -p ${impute2ResultDir}/${chr}/ - -${impute2Bin} \ --h ${referenceImpute2HapFile} \ --l ${referenceImpute2LegendFile} \ --m ${referenceImpute2MapFile} \ --g ${preparedStudyDir}/chr${chr}.gen \ --int ${fromChrPos} ${toChrPos} \ --o ${impute2ResultChrBinTemp} \ -2>&1 | tee -a ${impute2ResultChrBinLog} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - for tempFile in ${impute2ResultChrBinTemp}* ; do - finalFile=`echo $tempFile | sed -e "s/~//g"` - mv $tempFile $finalFile - done - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - -#Grep the log file, if there are no SNPs in this interval, three additional empty files will be created -#This to prevent the pipeline from crashing, since Impute2 doesn't produce these files when no SNPs available - - -if [ ! -f ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}_info ] -then - - echo "Touching file: ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}" - echo "Touching file: ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}_info" - echo "Touching file: ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}_info_by_sample" - - touch ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos} - touch ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}_info - touch ${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos}_info_by_sample - -fi - -putFile ${impute2ResultChrBin} -putFile ${impute2ResultChrBin}_info -putFile ${impute2ResultChrBin}_info_by_sample -putFile ${impute2ResultChrBin}_summary -putFile ${impute2ResultChrBin}_warnings - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/preparePedMapForImpute2.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/preparePedMapForImpute2.ftl deleted file mode 100644 index 74f1711121..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/preparePedMapForImpute2.ftl +++ /dev/null @@ -1,26 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${studyInputPedMapChr}.map -getFile ${studyInputPedMapChr}.ped - -inputs "${studyInputPedMapChr}.map" -inputs "${studyInputPedMapChr}.ped" -alloutputsexist "${studyPedMapChr}.map" \ -"${studyPedMapChr}.ped" - -mkdir -p ${studyPedMapChrDir} - -#Convert SNPids to chr_pos -awk '{$2=$1"_"$4; print $0}' ${studyInputPedMapChr}.map > ${studyPedMapChr}.map - -#Copy ped file -cp ${studyInputPedMapChr}.ped ${studyPedMapChr}.ped - -#Becarefull of phenotype field in ped files. Might crash later on -9 - -putFile ${studyPedMapChr}.map -putFile ${studyPedMapChr}.ped - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/prepareStudy.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/prepareStudy.ftl deleted file mode 100644 index f18e9f5601..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/protocols/prepareStudy.ftl +++ /dev/null @@ -1,77 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=8 - -#FOREACH project,chr - -getFile "${imputationToolJar}" -getFile "${imputationToolJsciCoreJar}" -getFile "${imputationToolGeneticaLibrariesJar}" - -getFile ${studyTriTyperChrDir}/GenotypeMatrix.dat -getFile ${studyTriTyperChrDir}/Individuals.txt -getFile ${studyTriTyperChrDir}/PhenotypeInformation.txt -getFile ${studyTriTyperChrDir}/SNPMappings.txt -getFile ${studyTriTyperChrDir}/SNPs.txt -getFile ${referenceTriTyperDir}/GenotypeMatrix.dat -getFile ${referenceTriTyperDir}/Individuals.txt -getFile ${referenceTriTyperDir}/PhenotypeInformation.txt -getFile ${referenceTriTyperDir}/SNPMappings.txt -getFile ${referenceTriTyperDir}/SNPs.txt - -inputs "${studyTriTyperChrDir}/GenotypeMatrix.dat" -inputs "${studyTriTyperChrDir}/Individuals.txt" -inputs "${studyTriTyperChrDir}/PhenotypeInformation.txt" -inputs "${studyTriTyperChrDir}/SNPMappings.txt" -inputs "${studyTriTyperChrDir}/SNPs.txt" -inputs "${referenceTriTyperDir}/GenotypeMatrix.dat" -inputs "${referenceTriTyperDir}/Individuals.txt" -inputs "${referenceTriTyperDir}/PhenotypeInformation.txt" -inputs "${referenceTriTyperDir}/SNPMappings.txt" -inputs "${referenceTriTyperDir}/SNPs.txt" -alloutputsexist "${preparedStudyDir}/chr${chr}.dat" \ -"${preparedStudyDir}/chr${chr}.map" \ -"${preparedStudyDir}/chr${chr}.markersbeagleformat" \ -"${preparedStudyDir}/chr${chr}.ped" \ -"${preparedStudyDir}/exportlog.txt" - -#If preparedStudyDir already exists delete it -if [ -d ${preparedStudyDir} ] -then - rm -r ${preparedStudyDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${preparedStudyTempDir} - - -java -Xmx8g -jar ${imputationToolJar} \ ---mode ttpmh \ ---in ${studyTriTyperChrDir} \ ---hap ${referenceTriTyperDir} \ ---out ${preparedStudyTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${preparedStudyTempDir} ${preparedStudyDir} - - putFile ${preparedStudyDir}/chr${chr}.dat - putFile ${preparedStudyDir}/chr${chr}.map - putFile ${preparedStudyDir}/chr${chr}.markersbeagleformat - putFile ${preparedStudyDir}/chr${chr}.ped - putFile ${preparedStudyDir}/exportlog.txt - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/workflowImpute.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/workflowImpute.csv deleted file mode 100644 index 1f116cfe16..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/impute2/workflowImpute.csv +++ /dev/null @@ -1,10 +0,0 @@ -name,protocol_name,PreviousSteps_name -impute2_s00,preparePedMapForImpute2, -impute2_s01,convertPedMapToTriTyper,impute2_s00 -impute2_s02,prepareStudy,impute2_s01 -impute2_s03,convertPreparedStudyPedMapToGen,impute2_s02 -impute2_s04,imputeWithImpute2,impute2_s03 -impute2_s05,concatImpute2ResultsPerChr,impute2_s04 -impute2_s06,convertConcatedImpute2ResultToPedMap,impute2_s05 -impute2_s07,calculateBeagleR2ForImpute2Results,impute2_s06 -impute2_s08,convertResultPedMapToB36,impute2_s06 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/imputeWithBeagle.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/imputeWithBeagle.ftl deleted file mode 100644 index cfc6f63b6f..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/imputeWithBeagle.ftl +++ /dev/null @@ -1,23 +0,0 @@ - - -#MOLGENIS walltime=72:00:00 nodes=1 cores=1 mem=35 - -#INPUTS beaglefile,beaglefilephased,markers -#OUTPUTS imputedoutputbeagle.* -#EXES beagle -#TARGETS project,chr - -inputs "${beaglefile}" -inputs "${beaglefilephased}" -inputs "${markers}" -alloutputsexist "${imputedoutputbeagle}" - - -#Impute using Beagle -java -jar -Xmx35g -Djava.io.tmpdir=${tempdir} \ -${beaglejar} \ -unphased=${beaglefile} \ -phased=${beaglefilephased} \ -markers=${markers} \ -missing=0 \ -out=${imputedoutputbeagle} \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/createWorkflowImpute.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/createWorkflowImpute.csv deleted file mode 100644 index 25bf3f924d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/createWorkflowImpute.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -createWorkflowImpute,createImputationScriptsAndWorksheet, \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/impute_with_minimach.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/impute_with_minimach.ftl deleted file mode 100644 index 11be1a62d7..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/impute_with_minimach.ftl +++ /dev/null @@ -1,28 +0,0 @@ -#OUTPUTS ${preparedStudyDir}/chr${chr}.results -#EXES minimacBin -#LOGS log -#TARGETS project,chr - -#FOREACH project,chr - -inputs "${vcfReference}.${chr}.vcf.gz" -inputs "${preparedStudyDir}/chr${chr}.gz" -inputs "${preparedStudyDir}/chr${chr}.dat" -alloutputsexist "${preparedStudyDir}/chr${chr}.results" - -#Minimac requires a file listing markers in the haplotype file. This file can be easily -#generated by extracting the second column from the .dat file. - -cut -f 2 -d " " ${preparedStudyDir}/chr${chr}.dat > ${preparedStudyDir}/chr${chr}.snps - -#Example -#cut -f 2 -d " " examples/sample.dat > examples/sample.snps - -#The imputation step -#TODO: Add ${minimacBin} to parameters.csv -#TODO: Add ${vcfReference} (/target/gpfs2/gcc/resources/ImputationReferenceSets/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL/chr10.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz) -${minimacBin} --vcfReference --refHaps ${vcfReference}.${chr}.vcf.gz --haps ${preparedStudyDir}/chr${chr}.gz --snps ${preparedStudyDir}/chr${chr}.snps --rounds 5 --states 200 --prefix ${preparedStudyDir}/chr${chr}.results - -#Example: -#./minimac --vcfReference --refHaps /target/gpfs2/gcc/resources/ImputationReferenceSets/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL/chr10.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --haps mach1.out.gz --snps examples/sample.snps --rounds 5 --states 200 --prefix results - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/parameters.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/parameters.csv deleted file mode 100644 index f798889b92..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/parameters.csv +++ /dev/null @@ -1,54 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -workflowFile,${McDir}/protocols/imputation/workflowBeagle.csv,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -plink,${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -#homedir,${root}/home/fvandijk,,, -homedir,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/,,, -projectdir,${homedir}/${project},,, -projectTempDir,${tempdir}/${McId}/${project}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyTriTyperTempDir,${projectTempDir}/~StudyTriTyper/,end with slash,, -studyTriTyperDir,${projectTempDir}/StudyTriTyper/,end with slash,, -preparedStudyTempDir,${projectTempDir}/~preparedStudy/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,${tooldir}/gtool_v0.7.5_x86_64>/gtool,,, -referenceFolder,${resdir}/imputation/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/,end with slash,, -referenceImpute2Dir,${referenceFolder}/${referencePanel}/Impute2/,end with slash,, -impute2Bin,${tooldir}/impute_v2.2.2_x86_64_static/impute2,,, -imputationToolJar,${tooldir}/ImputationTool/dist/ImputationTool2.jar,,, -referenceImpute2HapFile,${referenceImpute2Dir}/${chr}.hap -referenceImpute2LegendFile,${referenceImpute2Dir}/${chr}.legend -referenceImpute2MapFile,${referenceImpute2Dir}/${chr}.map -impute2ResultDir,${projectTempDir}/Impute2Result/,end with slash,, -calculateBeagleR2ForIMpute2ResultsPythonScript,${tooldir}/python_scripts/calculateBeagleR2ForImpute2Results.py,,, -impute2ResultChrBinTemp,${impute2ResultDir}/${chr}/~chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBin,${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBinGenFile,${impute2ResultChrBin}.gen,Ask alex for correct file extension,, -impute2ResultChrBinInfoFile,${impute2ResultChrBin}.info,,, -project,,,,"imputationResult,studyInputPedMap,referencePanel" \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/phase_study_with_mach.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/phase_study_with_mach.ftl deleted file mode 100644 index c9bc5749b1..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/mach_minimach/phase_study_with_mach.ftl +++ /dev/null @@ -1,24 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#INPUTS preparedStudyDir/chr${chr}.ped,preparedStudyDir/chr${chr}.dat -#OUTPUTS preparedStudyDir/chr${chr}.gz -#EXES machBin -#LOGS log -#TARGETS project,chr - -#FOREACH project,chr - -inputs "${preparedStudyDir}/chr${chr}.ped" -inputs "${preparedStudyDir}/chr${chr}.dat" -alloutputsexist "${preparedStudyDir}/chr${chr}.gz" - - -#Use mach to phase the study panel. The command should be like -#TODO: We have to define machBin in parameters.csv -${machBin} -d ${preparedStudyDir}/chr${chr}.dat -p ${preparedStudyDir}/chr${chr}.ped --rounds 20 --states 20 --phase --interim 5 --compact --prefix ${preparedStudyDir}/~chr${chr} - -#Example -# ./executables/mach1 -d examples/sample.dat -p examples/sample.ped --rounds 20 --states 20 --phase --interim 5 --compact - -#Remove intermediate preliminary data if the previous step was correct -rm ${preparedStudyDir}/~chr${chr}.prelim* diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/exampleWorksheet.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/exampleWorksheet.csv deleted file mode 100644 index 8881fd0b4d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/exampleWorksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,studyInputDir,referencePanel,imputationResultDir,imputationPipeline,genomeBuild,chr,autostart -1240Blood_b37,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood_b37/,gonl_release3.1,${root}/home/fvandijk/minimac/test2,minimac,b37,20,TRUE diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/parametersMinimac.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/parametersMinimac.csv deleted file mode 100644 index 1fa056cfe5..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/parametersMinimac.csv +++ /dev/null @@ -1,97 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,default,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc/,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -resdir,${root}/resources,,, -#,,,, -tempdir,${imputationResultDir}/tmp/,,, -plink,${tooldir}/plink-${plinkversion}/plink,,, -plinkversion,1.07-x86_64,,, -plinkseqBin,${tooldir}/plink-${plinkseqversion}/plink108,,, -plinkseqversion,1.08,,, -projectPhasingJobsDir,${McScripts}/../phasing/,,, -projectImputationJobsDir,${McScripts}/../imputation/,,, -projectPhasingJobsDirTarGz,${McScripts}/../phasing.tar.gz,,, -projectImputationJobsDirTarGz,${McScripts}/../imputation.tar.gz,,, -projectTempDir,${tempdir}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyInputPedMapChr,${studyInputDir}/chr${chr},,, -studyPedMapChrDir,${studyPedMapDir}/chr${chr}/,,, -studyPedMapChr,${studyPedMapChrDir}/chr${chr},,, -studyTriTyperChrTempDir,${projectTempDir}/StudyTriTyper/~chr${chr}/,end with slash,, -studyTriTyperChrDir,${projectTempDir}/StudyTriTyper/chr${chr}/,end with slash,, -preparedStudyTempDir,${projectTempDir}/preparedStudy/~${chr}/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/${chr}/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,gtool,,, -#gtoolBin,${tooldir}/gtool_${gtoolBinversion}/gtool,,, -gtoolBinversion,v0.7.5_x86_64,,, -referenceFolder,${resdir}/imputationReference/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/Chr${chr}/,end with slash,, -pythonversion,2.7.3,,, -javaversion,1.6.0_33,,, -imputationToolJar,${tooldir}/ImputationTool-${imputationToolJarversion}/ImputationTool.jar,,, -imputationToolJarversion,20120912,,, -imputationToolLibDir,${tooldir}/ImputationTool-${imputationToolJarversion}/lib/,,, -imputationToolGeneticaLibrariesJar,${imputationToolLibDir}/GeneticaLibraries.jar,,, -imputationToolJsciCoreJar,${imputationToolLibDir}/jsci-core-1.1.jar,,, -convertB36ChrTempDir,${projectTempDir}/b36conversion/,,, -convertB36ChrHg19Bed,${convertB36ChrTempDir}/chr_${chr}Hg19.bed,,, -convertB36unmapped,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -convertB36unmappedSNPs,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -b36conversionPedMapResultDir,${imputationResultDir}/b36PedMap/,,, -liftOverUcscBin,${tooldir}/liftOverUcsc-${liftOverUcscBinversion}/liftOver,,, -liftOverUcscBinversion,20120905,,, -convertB36ChrHg18Bed,${convertB36ChrTempDir}/chr_${chr}Hg18.bed,,, -liftoverDir,${resdir}/liftover/,,, -hg19ToHg18chainfile,${liftoverDir}/hg19ToHg18.over.chain,,, -project,,,,"imputationResultDir,studyInputDir,referencePanel,imputationPipeline" -expandWorksheetJar,${tooldir}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}.jar,,, -expandWorksheetJarversion,V1.1,,, -concatWorksheetsJar,${tooldir}/ConcatWorksheets${concatWorksheetsJarversion}/ConcatWorksheets${concatWorksheetsJarversion}.jar -concatWorksheetsJarversion,V1.0,,, -#,,,, -chr,,,, -chunkSize,2000,,, -chunkOverlap,750,,, -chunkChromosomeBin,${tooldir}/ChunkChromosome-${chunkChromosomeBinVersion}/ChunkChromosome,,, -chunkChromosomeBinVersion,2012-08-28,,, -chunk,,,, -chunkChrWorkSheet,${tempdir}/tmpChr${chr}ChunkWorksheet.csv,,, -finalChunkChrWorksheet,${tempdir}/ChunkChr${chr}Worksheet.csv,,, -tmpFinalChunkChrWorksheet,${tempdir}/~ChunkChr${chr}Worksheet.csv,,, -concattedChunkWorksheet,${McScripts}/../concattedChunkWorksheet.csv,,, -tmpConcattedChunkWorksheet,${McScripts}/../~concattedChunkWorksheet.csv,,, -studyMerlinDir,${tempdir}/studyMerlin/,,, -studyMerlinChrDir,${studyMerlinDir}/chr${chr}/,,, -studyMerlinChrMap,${studyMerlinChrDir}/chr${chr}.map,,, -studyMerlinChrDat,${studyMerlinChrDir}/chr${chr}.dat,,, -studyMerlinChrPed,${studyMerlinChrDir}/chr${chr}.ped,,, -machBin,${tooldir}/mach.${machBinversion}/executables/mach1,,, -machBinversion,1.0.18,,, -studyChunkDir,${tempdir}/studyChunks,,, -studyChunkChrDir,${studyChunkDir}/chr${chr}/,,, -phasingRounds,20,,, -phasingStates,200,,, -phasingHaplotypeSampling,5,,, -minimacOmpBin,${tooldir}/minimac-beta-${minimacVersion}/minimac-omp,,, -minimacBin,${tooldir}/minimac-beta-${minimacVersion}/minimac,,, -minimacVersion,2012.10.3,,, -referenceChrVcf,${referenceFolder}/${referencePanel}/vcf/chr${chr}.vcf,,, -referenceChrVcfGz,${referenceFolder}/${referencePanel}/vcf/chr${chr}.vcf.gz,,, -#,,,, -studyInputDir,,,, -referencePanel,,,, -imputationResultDir,,,, -imputationPipeline,,,, -genomeBuild,,,, -autostart,TRUE,,, diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index 15513f7867..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 0 - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Footer.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Header.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Header.ftl deleted file mode 100644 index 32e91a79b6..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Header.ftl +++ /dev/null @@ -1,34 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#!/bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - -<#elseif scheduler == "GRID"> - - - - -<#if scheduler != "GRID"> -# Configures the GCC bash environment -. ${root}/gcc.bashrc - - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Helpers.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Macros.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/NGSHeader.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/chunkChromosome.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/chunkChromosome.ftl deleted file mode 100644 index e6d7b33280..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/chunkChromosome.ftl +++ /dev/null @@ -1,85 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${chunkChromosomeBin} -getFile ${expandWorksheetJar} - -getFile ${studyMerlinChrDat} -getFile ${McWorksheet} - -inputs "${studyMerlinChrDat}" -inputs "${McWorksheet}" - - -#!!!! -#alloutputsexist \ -# "${studyMerlinChrDir}/chunk$c-chr${chr}.dat.snps" \ -$ "${studyMerlinChrDir}/chunk$c-chr${chr}.dat" - -#Chunk chromosomes into pieces containing ~${chunkSize} markers - -cd ${studyMerlinChrDir} - -${chunkChromosomeBin} \ - -d ${studyMerlinChrDat} \ - -n ${chunkSize} \ - -o ${chunkOverlap} - -returnCode=$? - -if [ $returnCode -ne 0 ] -then - - echo -e "\nNon zero return code. Something went wrong creating the chunks\n\n" - #Return non zero return code - exit 1 - -fi - -#Create .csv file to be merged with original worksheet -echo "chunk" > ${chunkChrWorkSheet} - - -chunks=(${studyMerlinChrDir}/chunk*-chr${chr}.dat.snps) - -s=${r"${#chunks[*]}"} - -for c in `seq 1 $s` -do - echo $c >> ${chunkChrWorkSheet} - putFile ${studyMerlinChrDir}/chunk$c-chr${chr}.dat.snps - putFile ${studyMerlinChrDir}/chunk$c-chr${chr}.dat -done - - -#Merge worksheets -module load jdk/${javaversion} - -#Run Jar to create full worksheet - - -java -jar ${expandWorksheetJar} ${McWorksheet} ${tmpFinalChunkChrWorksheet} ${chunkChrWorkSheet} project ${project} chr ${chr} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${tmpFinalChunkChrWorksheet} ${finalChunkChrWorksheet} - - putFile ${finalChunkChrWorksheet} - - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/convertPedMapToTriTyper.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/convertPedMapToTriTyper.ftl deleted file mode 100644 index 62ad8ba171..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/convertPedMapToTriTyper.ftl +++ /dev/null @@ -1,61 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${imputationToolJar} -getFile ${imputationToolJsciCoreJar} -getFile ${imputationToolGeneticaLibrariesJar} - -getFile ${studyPedMapChr}.map -getFile ${studyPedMapChr}.ped - - - -inputs "${studyPedMapChr}.map" -inputs "${studyPedMapChr}.ped" -alloutputsexist "${studyTriTyperChrDir}/GenotypeMatrix.dat" \ - "${studyTriTyperChrDir}/Individuals.txt" \ - "${studyTriTyperChrDir}/PhenotypeInformation.txt" \ - "${studyTriTyperChrDir}/SNPMappings.txt" \ - "${studyTriTyperChrDir}/SNPs.txt" - - -if [ -d ${studyTriTyperChrDir} ] -then - rm -r ${studyTriTyperChrDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${studyTriTyperChrTempDir} - -java -jar ${imputationToolJar} \ - --mode pmtt \ - --in ${studyPedMapChrDir} \ - --out ${studyTriTyperChrTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${studyTriTyperChrTempDir} ${studyTriTyperChrDir} - - putFile "${studyTriTyperChrDir}/GenotypeMatrix.dat" - putFile "${studyTriTyperChrDir}/Individuals.txt" - putFile "${studyTriTyperChrDir}/PhenotypeInformation.txt" - putFile "${studyTriTyperChrDir}/SNPMappings.txt" - putFile "${studyTriTyperChrDir}/SNPs.txt" - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/convertPlinkPedMapToMerlin.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/convertPlinkPedMapToMerlin.ftl deleted file mode 100644 index 1fb7d457bc..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/convertPlinkPedMapToMerlin.ftl +++ /dev/null @@ -1,38 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${preparedStudyDir}/chr${chr}.map -getFile ${preparedStudyDir}/chr${chr}.ped -getFile ${studyPedMapChr}.ped - -inputs ${preparedStudyDir}/chr${chr}.map -inputs ${preparedStudyDir}/chr${chr}.ped -inputs ${studyPedMapChr}.ped - - -alloutputsexist \ -"${studyMerlinChrMap}" \ -"${studyMerlinChrDat}" \ -"${studyMerlinChrPed}" - -mkdir -p ${studyMerlinChrDir} - -#Conver SNP ID to chr_pos and remove 3e column to adhere to merlin -gawk ' - BEGIN {$1="CHROMOSOME";$2="MARKER";$3="POSITION";print $0} - {$2=$1":"$4;print $1,$2,$4} -' OFS="\t" ${preparedStudyDir}/chr${chr}.map > ${studyMerlinChrMap} - -gawk 'BEGIN {print "T","pheno";}{print "M",$1":"$4}' ${preparedStudyDir}/chr${chr}.map > ${studyMerlinChrDat} - -set +o posix - -#Create merlin ped from genotypes outputed by imputation tool but use fam id, sample id and phenodata from original pedmap -paste <(awk '{print $1,$2,$3,$4,$5,$6}' ${studyPedMapChr}.ped) <(awk '{for(i=7;i ${studyMerlinChrPed} - -putFile ${studyMerlinChrMap} -putFile ${studyMerlinChrDat} -putFile ${studyMerlinChrPed} - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/mergeMinimacImputationResults.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/mergeMinimacImputationResults.ftl deleted file mode 100644 index 2ec45b2492..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/mergeMinimacImputationResults.ftl +++ /dev/null @@ -1,62 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -Fix in- and outputs later -#getFile - -#Retrieve number of chunks (list) -s=${chunk?size} - - -##Paste resulting chunk *.impuated.dose files together -cp ${studyChunkChrDir}/chunk1-chr${chr}.imputed.dose ${studyChunkChrDir}/chunk1-chr${chr}.imputed.dose.tmp - -<#assign x=chunk?size+1> - -<#if x gt 1> -for c in `seq 2 $s` -do - cut -f3- ${studyChunkChrDir}/chunk$c-chr${chr}.imputed.dose \ - > ${studyChunkChrDir}/chunk$c-chr${chr}.imputed.dose.tmp -done - - -paste \ -<#list chunk as chnk> -${studyChunkChrDir}/chunk${chnk}-chr${chr}.imputed.dose.tmp \ - -> ${imputationResultDir}/chr${chr}.imputed.merged.dose - -#Concat *.rec and *.info chunk files - -<#assign x=chunk?size+1> - -<#if x gt 1> -( cat ${studyChunkChrDir}/chunk1-chr${chr}.imputed.info <#list 2..x as chnk><#if chnk_has_next>; tail -n +2 ${studyChunkChrDir}/chunk${chnk}-chr${chr}.imputed.info ) \ ->> ${imputationResultDir}/chr${chr}.imputed.merged.info - - - -#Create *.fam file from *.imputed.dose and original ped file - -awk '{print $1}' ${studyChunkChrDir}/chunk1-chr${chr}.imputed.dose \ -| awk '{print $1,$2}' FS="->" OFS="_" > ${studyChunkChrDir}/chr${chr}_fam_sample.txt - -awk '{$7=$1"_"$2;print $7,$1,$2,$3,$4,$5,$6}' \ -${studyPedMapChr}.ped \ -> ${studyChunkChrDir}/chr${chr}.tmp.ped - -awk ' FILENAME=="${studyChunkChrDir}/chr${chr}.tmp.ped" \ -{arr[$1]=$0; next} FILENAME=="${studyChunkChrDir}/chr${chr}_fam_sample.txt" \ -{print arr[$1]} ' ${studyChunkChrDir}/chr${chr}.tmp.ped \ -${studyChunkChrDir}/chr${chr}_fam_sample.txt \ -| awk '{print $1,$2,$3,$4,$5,$6,$7}' \ -| awk '{ -if ($0 ~ /^[ ]*$/) \ - print "FamilyID_SampleID combination not found in original PED file!" > "/dev/stderr" - exit 1; \ -else - print $2,$3,$4,$5,$6,$7}' \ -> ${imputationResultDir}/chr${chr}.fam - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/minimacImputation.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/minimacImputation.ftl deleted file mode 100644 index e0b49de81b..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/minimacImputation.ftl +++ /dev/null @@ -1,61 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr,chunk - -getFile ${minimacBin} - -getFile ${referenceChrVcf} -getFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz -getFile ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps - -inputs "${referenceChrVcf}" -inputs "${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz" -inputs "${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps" - -alloutputsexist \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.dose \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.erate \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info.draft \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.rec \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log - - -${minimacBin} \ - --refHaps ${referenceChrVcf} \ - --vcfReference \ - --haps ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz \ - --snps ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps \ - --prefix ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed \ - --autoClip ${studyMerlinChrDir}/autoChunk-chr${chr}.dat \ - 2>&1 | tee ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed-minimac.log - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.dose ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.dose - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.erate ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.erate - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.info ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.info.draft ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info.draft - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.rec ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.rec - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed-minimac.log ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log - - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.dose - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.erate - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info.draft - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.rec - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/phaseChunk.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/phaseChunk.ftl deleted file mode 100644 index cb54764bcf..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/phaseChunk.ftl +++ /dev/null @@ -1,56 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr,chunk - -getFile ${machBin} - -getFile ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat -getFile ${studyMerlinChrPed} - -inputs "${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat" -inputs "${studyMerlinChrPed}" - -alloutputsexist \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate" \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz" \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec" \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log" - - -mkdir -p ${studyChunkChrDir} - -${machBin} \ - -d ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat \ - -p ${studyMerlinChrPed} \ - --prefix ${studyChunkChrDir}/~chunk${chunk}-chr${chr} \ - --rounds ${phasingRounds} \ - --states ${phasingStates} \ - --phase \ - 2>&1 | tee -a ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.erate ${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.gz ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.rec ${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}-mach.log ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/preparePedMapForImputationTool.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/preparePedMapForImputationTool.ftl deleted file mode 100644 index 9d5151c04e..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/preparePedMapForImputationTool.ftl +++ /dev/null @@ -1,23 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${studyInputPedMapChr}.map -getFile ${studyInputPedMapChr}.ped - -inputs "${studyInputPedMapChr}.map" -inputs "${studyInputPedMapChr}.ped" -alloutputsexist \ - "${studyPedMapChr}.map" \ - "${studyPedMapChr}.ped" - -mkdir -p ${studyPedMapChrDir} - -#Convert SNPids to chr_pos -awk '{$2=$1"_"$4; print $0}' ${studyInputPedMapChr}.map > ${studyPedMapChr}.map - -#Copy ped file -cp ${studyInputPedMapChr}.ped ${studyPedMapChr}.ped - -putFile ${studyPedMapChr}.map -putFile ${studyPedMapChr}.ped diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/prepareStudy.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/prepareStudy.ftl deleted file mode 100644 index f67d397d27..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/prepareStudy.ftl +++ /dev/null @@ -1,77 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=8 - -#FOREACH project,chr - -getFile ${imputationToolJar} -getFile ${imputationToolJsciCoreJar} -getFile ${imputationToolGeneticaLibrariesJar} - -getFile ${studyTriTyperChrDir}/GenotypeMatrix.dat -getFile ${studyTriTyperChrDir}/Individuals.txt -getFile ${studyTriTyperChrDir}/PhenotypeInformation.txt -getFile ${studyTriTyperChrDir}/SNPMappings.txt -getFile ${studyTriTyperChrDir}/SNPs.txt -getFile ${referenceTriTyperDir}/GenotypeMatrix.dat -getFile ${referenceTriTyperDir}/Individuals.txt -getFile ${referenceTriTyperDir}/PhenotypeInformation.txt -getFile ${referenceTriTyperDir}/SNPMappings.txt -getFile ${referenceTriTyperDir}/SNPs.txt - -#inputs "${studyTriTyperChrDir}/GenotypeMatrix.dat" -#inputs "${studyTriTyperChrDir}/Individuals.txt" -#inputs "${studyTriTyperChrDir}/PhenotypeInformation.txt" -#inputs "${studyTriTyperChrDir}/SNPMappings.txt" -#inputs "${studyTriTyperChrDir}/SNPs.txt" -inputs "${referenceTriTyperDir}/GenotypeMatrix.dat" -inputs "${referenceTriTyperDir}/Individuals.txt" -inputs "${referenceTriTyperDir}/PhenotypeInformation.txt" -inputs "${referenceTriTyperDir}/SNPMappings.txt" -inputs "${referenceTriTyperDir}/SNPs.txt" -alloutputsexist "${preparedStudyDir}/chr${chr}.dat" \ -"${preparedStudyDir}/chr${chr}.map" \ -"${preparedStudyDir}/chr${chr}.markersbeagleformat" \ -"${preparedStudyDir}/chr${chr}.ped" \ -"${preparedStudyDir}/exportlog.txt" - -#If preparedStudyDir already exists delete it -if [ -d ${preparedStudyDir} ] -then - rm -r ${preparedStudyDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${preparedStudyTempDir} - - -java -Xmx8g -jar ${imputationToolJar} \ ---mode ttpmh \ ---in ${studyTriTyperChrDir} \ ---hap ${referenceTriTyperDir} \ ---out ${preparedStudyTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${preparedStudyTempDir} ${preparedStudyDir} - - putFile ${preparedStudyDir}/chr${chr}.dat - putFile ${preparedStudyDir}/chr${chr}.map - putFile ${preparedStudyDir}/chr${chr}.markersbeagleformat - putFile ${preparedStudyDir}/chr${chr}.ped - putFile ${preparedStudyDir}/exportlog.txt - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/startMinimacStage2.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/startMinimacStage2.ftl deleted file mode 100644 index c869caddb5..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/startMinimacStage2.ftl +++ /dev/null @@ -1,98 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH autostart - -getFile ${concatWorksheetsJar} - -<#list finalChunkChrWorksheet as chunkFile> - getFile ${chunkFile} - - - -inputs "${ssvQuoted(finalChunkChrWorksheet)}" -alloutputsexist \ - "${projectPhasingJobsDir}/check_for_submission.txt" \ - "${concattedChunkWorksheet}" \ - "${projectPhasingJobsDirTarGz}" - - -module load jdk/${javaversion} - -java -jar ${concatWorksheetsJar} \ - ${tmpConcattedChunkWorksheet} \ - ${ssvQuoted(finalChunkChrWorksheet)} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${tmpConcattedChunkWorksheet} ${concattedChunkWorksheet} - - putFile ${concattedChunkWorksheet} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - -#Call compute to generate phasing jobs - -mkdir -p ${projectPhasingJobsDir} - -# Execute MOLGENIS/compute to create job scripts. -sh ${McDir}/molgenis_compute.sh \ --worksheet="${concattedChunkWorksheet}" \ --parameters="${McParameters}" \ --workflow="${McProtocols}/../workflowMinimacStage2.csv" \ --protocols="${McProtocols}/" \ --templates="${McTemplates}/" \ --scripts="${projectPhasingJobsDir}/" \ --id="${McId}" - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nJob generation succesful!\n\n" - - perl -pi -e "s/sleep 8/sleep 0/" ${projectPhasingJobsDir}/submit.sh - - <#if autostart == "TRUE"> - cd ${projectPhasingJobsDir} - sh submit.sh - touch ${projectPhasingJobsDir}/check_for_submission.txt - <#elseif autostart == "FALSE"> - - echo "No autostart selected" - - echo "You can submit your jobs using the following command:" - echo "cd ${projectPhasingJobsDir}" - echo "sh submit.sh" - - - - - tar czf ${projectPhasingJobsDirTarGz} ${projectPhasingJobsDir} - putFile ${projectPhasingJobsDirTarGz} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/startMinimacStage3.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/startMinimacStage3.ftl deleted file mode 100644 index 84ccc247c5..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/protocols/startMinimacStage3.ftl +++ /dev/null @@ -1,73 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH autostart - -getFile ${expandWorksheetJar} - -getFile ${concattedChunkWorksheet} - -inputs "${concattedChunkWorksheet}" -alloutputsexist \ -"${projectImputationJobsDirTarGz}" \ -${projectImputationJobsDir}/check_for_submission.txt - - - - -#Call compute to generate phasing jobs -module load jdk/${javaversion} - -mkdir -p ${projectImputationJobsDir} - -# Execute MOLGENIS/compute to create job scripts. -sh ${McDir}/molgenis_compute.sh \ --worksheet="${concattedChunkWorksheet}" \ --parameters="${McParameters}" \ --workflow="${McProtocols}/../workflowMinimacStage3.csv" \ --protocols="${McProtocols}/" \ --templates="${McTemplates}/" \ --scripts="${projectImputationJobsDir}/" \ --id="${McId}" - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nJob generation succesful!\n\n" - - perl -pi -e "s/sleep 8/sleep 0/" ${projectImputationJobsDir}/submit.sh - - <#if autostart == "TRUE"> - cd ${projectImputationJobsDir} - sh submit.sh - - touch ${projectImputationJobsDir}/check_for_submission.txt - - <#elseif autostart == "FALSE"> - - echo "No autostart selected" - - echo "You can submit your jobs using the following command:" - echo "cd ${projectImputationJobsDir}" - echo "sh submit.sh" - - - - - - tar czf ${projectImputationJobsDirTarGz} ${projectImputationJobsDir} - putFile ${projectImputationJobsDirTarGz} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage1.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage1.csv deleted file mode 100644 index 0afec2b920..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage1.csv +++ /dev/null @@ -1,7 +0,0 @@ -name,protocol_name,PreviousSteps_name -prePhasingMach_s00,preparePedMapForImputationTool, -prePhasingMach_s01,convertPedMapToTriTyper,prePhasingMach_s00 -prePhasingMach_s02,prepareStudy,prePhasingMach_s01 -prePhasingMach_s03,convertPlinkPedMapToMerlin,prePhasingMach_s02 -prePhasingMach_s04,chunkChromosome,prePhasingMach_s03 -prePhasingMach_s05,startMinimacStage2,prePhasingMach_s04 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage2.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage2.csv deleted file mode 100644 index 34d168fcf9..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage2.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -prePhasingMachStage2_s00,phaseChunk, -prePhasingMachStage2_s01,startMinimacStage3,prePhasingMachStage2_s00 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage3.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage3.csv deleted file mode 100644 index 16f01679a7..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/minimac/workflowMinimacStage3.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -imputationMinimac_s00,minimacImputation, -imputationMinimac_s01,mergeMinimacImputationResults,imputationMinimac_s00 diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/myProject.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/myProject.csv deleted file mode 100644 index d0d94a82f2..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/myProject.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,chr -1240Blood_b37Test,20 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/parameters.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/parameters.csv deleted file mode 100644 index a665be0e4d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/parameters.csv +++ /dev/null @@ -1,42 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -workflowFile,${McDir}/protocols/imputation/workflowBeagle.csv,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -plink,${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -#homedir,${root}/home/fvandijk,,, -homedir,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/,,, -projectdir,${homedir}/${project},,, -plinkdata,${projectdir}/${chr},,, -plinkdatatransposed,${plinkdata}.transposed,,, -beaglefile,${plinkdata}.bgl,,, -beaglefilephased,/target/gpfs2/gcc/home/fvandijk/gonl_beagle_phased/bgl-likelihoods.gonl.20.biallelic.VA.vqsr.bgl.phased,Comes from samplesheet,, -markerspt1,${plinkdata}.markers1.txt,,, -markerspt2,${plinkdata}.markers2.txt,,, -markers,${plinkdata}.markers.txt,,, -imputedoutputbeagle,${plinkdata}.imputed,,, -beaglejar,${tooldir}/beagle_3.3_26Dec10/beagle.jar,,, -convertbgltotrityperjar,${tooldir}/BeagleSingleFileConvertToTriTyper/dist/BeagleSingleFileConvertToTriTyper.jar,,, -bgltotrityperoutput,${projectdir}/TriTyperOutput/,The trailing backslash is obligatory!,, diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/CustomSubmit.sh.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Footer.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Header.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Header.ftl deleted file mode 100644 index 56d943bf8a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Header.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#!/bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - - - - - -# Configures the GCC bash environment -. ${root}/gcc.bashrc - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Helpers.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Macros.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/NGSHeader.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/convertReferenceVcfSnpId.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/convertReferenceVcfSnpId.ftl deleted file mode 100644 index cca5eb7e88..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/convertReferenceVcfSnpId.ftl +++ /dev/null @@ -1,25 +0,0 @@ -#MOLGENIS walltime=06:00:00 nodes=1 cores=1 mem=1 - -inputs ${chrVcfReferenceIntermediateFile} -alloutputsexist ${chrVcfReferenceFile} - -mkdir -p ${vcfReferenceFolder} - -perl ${convertVcfIdsScript} -inputvcf ${chrVcfReferenceIntermediateFile} -outputvcf ${chrVcfReferenceFileTmp} -delimiter ${convertVcfIdsScriptDelimiter} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - mv ${chrVcfReferenceFileTmp} ${chrVcfReferenceFile} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/createImpute2Reference.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/createImpute2Reference.ftl deleted file mode 100644 index 22ab52fe9d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/createImpute2Reference.ftl +++ /dev/null @@ -1,34 +0,0 @@ -#MOLGENIS walltime=06:00:00 nodes=1 cores=1 mem=1 - -inputs ${chrVcfReferenceFile} -alloutputsexist ${chrImpute2Hap} -alloutputsexist ${chrImpute2HapIndv} -alloutputsexist ${chrImpute2HapLegend} -alloutputsexist ${chrImpute2HapLog} - - -mkdir -p ${impute2Folder} - - -${vcftoolsBin} --vcf ${chrVcfReferenceFile} --out ${impute2Folder}/~${chr} --IMPUTE - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - for tempFile in ${impute2Folder}/~${chr}.* ; do - finalFile=`echo $tempFile | sed -e "s/~//g"` - mv $tempFile $finalFile - done - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/filterVcf.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/filterVcf.ftl deleted file mode 100644 index 6398374031..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/filterVcf.ftl +++ /dev/null @@ -1,34 +0,0 @@ -#MOLGENIS walltime=06:00:00 nodes=1 cores=1 mem=1 - -sleep 120 - -inputs ${chrVcfInputFile} -alloutputsexist ${chrVcfReferenceIntermediateFile} - -mkdir -p ${tmpFolder} - - - - -<#assign lengthVcfPath = chrVcfInputFile?length> -<#assign isGz = chrVcfInputFile?substring(lengthVcfPath - 2, lengthVcfPath) == "gz"> - - -${vcftoolsBin} <#if isGz> --gzvcf <#else> --vcf ${chrVcfInputFile} --out ${tmpFolder}/~chr${chr} <#if samplesToIncludeFile != ""> --keep ${samplesToIncludeFile} ${vcfFilterOptions} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - mv ${chrVcfReferenceIntermediateFileTemp} ${chrVcfReferenceIntermediateFile} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/parameters.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/parameters.csv deleted file mode 100644 index ebc4e369e9..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/parameters.csv +++ /dev/null @@ -1,44 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,gcc,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -#,,,, -referenceFolder,${resdir}/imputationReference/${referenceName}/,,, -tmpFolder,${referenceFolder}/tmp/,,, -vcfReferenceFolder,${referenceFolder}/vcf/,,, -chrVcfReferenceIntermediateFileTemp,${tmpFolder}/~chr${chr}.recode.vcf,,, -chrVcfReferenceIntermediateFile,${tmpFolder}/chr${chr}.recode.vcf,,, -vcftoolsBin,${tooldir}/vcftools_0.1.9/bin/vcftools,,, -chrVcfReferenceFileTmp,${vcfReferenceFolder}/~chr${chr}.vcf,,, -chrVcfReferenceFile,${vcfReferenceFolder}/chr${chr}.vcf,,, -triTyperFolder,${referenceFolder}/TriTyper/,,, -triTyperFolderTemp,${referenceFolder}/~TriTyper/,end with slash,, -chrTriTyperFolder,${triTyperFolder}/Chr${chr}/,,, -convertVcfIdsScript,${scriptdir}/convert_snpIDsV2.pl,,, -convertVcfIdsScriptDelimiter,_,,, -impute2Folder,${referenceFolder}/Impute2/,,, -#,,,, -#,,Output files,, -#,,,, -chrVcfReferenceFile,${vcfReferenceFolder}/chr${chr}.vcf,,, -chrTriTyperGenotypeMatrix,${chrTriTyperFolder}/GenotypeMatrix.dat,,, -chrTriTyperIndividuals,${chrTriTyperFolder}/Individuals.txt,,, -chrTriTyperPhenotypeInformation,${chrTriTyperFolder}/PhenotypeInformation.txt,,, -chrTriTyperSNPMappings,${chrTriTyperFolder}/SNPMappings.txt,,, -chrTriTyperSNPs,${chrTriTyperFolder}/SNPs.txt,,, -chrImpute2Hap,${impute2Folder}/${chr}.impute.hap,,, -chrImpute2HapIndv,${impute2Folder}/${chr}.impute.hap.indv,,, -chrImpute2HapLegend,${impute2Folder}/${chr}.impute.legend,,, -chrImpute2HapLog,${impute2Folder}/${chr}.log,,, - diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/prepareReferenceWorkflow.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/prepareReferenceWorkflow.csv deleted file mode 100644 index 7b9f10d692..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/prepareReferenceWorkflow.csv +++ /dev/null @@ -1,5 +0,0 @@ -name,protocol_name,PreviousSteps_name -filterVcf,filterVcf, -convertReferenceVcfSnpId,convertReferenceVcfSnpId,filterVcf -vcfToTriTyperReference,vcfToTriTyperReference,convertReferenceVcfSnpId -createImpute2Reference,createImpute2Reference,convertReferenceVcfSnpId \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/prepareReferenceWorksheetSample.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/prepareReferenceWorksheetSample.csv deleted file mode 100644 index e77f78864a..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/prepareReferenceWorksheetSample.csv +++ /dev/null @@ -1,3 +0,0 @@ -referenceName,chrVcfInputFile,chr,samplesToIncludeFile,vcfFilterOptions -test,/target/gpfs2/gcc/groups/gonl/projects/trio-analysis/results/snps/release3/gonl.chr${chr}.release3.1.vcf,20,sdfsdf,--recode --remove-indels --remove-filtered-all --mac 1 --min-alleles 2 --max-alleles 2 -test,/target/gpfs2/gcc/groups/gonl/projects/trio-analysis/results/snps/release3/gonl.chr${chr}.release3.1.vcf,21,sdfsdf,--recode --remove-indels --remove-filtered-all --mac 1 --min-alleles 2 --max-alleles 2 \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/vcfToTriTyperReference.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/vcfToTriTyperReference.ftl deleted file mode 100644 index 9811f44a0d..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/prepareReference/vcfToTriTyperReference.ftl +++ /dev/null @@ -1,32 +0,0 @@ -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=1 - -#FOREACH referenceName - -inputs ${ssvQuoted(chrVcfReferenceFile)} -alloutputsexist ${ssvQuoted(chrTriTyperGenotypeMatrix)} -alloutputsexist ${ssvQuoted(chrTriTyperIndividuals)} -alloutputsexist ${ssvQuoted(chrTriTyperPhenotypeInformation)} -alloutputsexist ${ssvQuoted(chrTriTyperSNPMappings)} -alloutputsexist ${ssvQuoted(chrTriTyperSNPs)} - -mkdir -p ${triTyperFolderTemp} - - -java -jar ~/Programs/ConvertVcfToTriTyper.jar ${vcfReferenceFolder} ${triTyperFolderTemp} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - mv ${triTyperFolderTemp} ${triTyperFolder} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/transposePlinkData.ftl b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/transposePlinkData.ftl deleted file mode 100644 index 7355b94209..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/transposePlinkData.ftl +++ /dev/null @@ -1,50 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS plinkdata -#OUTPUTS plinkdatatransposed -#EXES plink -#TARGETS project,chr - -inputs "${plinkdata}.bed" -inputs "${plinkdata}.bim" -inputs "${plinkdata}.fam" -alloutputsexist "${plinkdatatransposed}.tfam" -alloutputsexist "${plinkdatatransposed}.tped" - - - - - -#Transpose plink data -${plink} \ ---bfile ${plinkdata} \ ---chr ${chr} \ ---transpose \ ---recode \ ---out ~${plinkdatatransposed} \ ---noweb - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - - echo -e "\nMoving temp files to final files\n\n" - - for tempFile in ${plinkdatatransposed}* ; do - finalFile=`echo $tempFile | sed -e "s/~//g"` - mv $tempFile $finalFile - done - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/workflowBeagle.csv b/modules/compute/demo/debugFolding/inputdir/protocols/imputation/workflowBeagle.csv deleted file mode 100644 index 9414cfa292..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/protocols/imputation/workflowBeagle.csv +++ /dev/null @@ -1,6 +0,0 @@ -name,protocol_name,PreviousSteps_name -transposePlinkData,transposePlinkData, -createBglFileFromPlinkData,createBglFileFromPlinkData,transposePlinkData -createMarkerFile,createMarkerFile,createBglFileFromPlinkData -imputeWithBeagle,imputeWithBeagle,createMarkerFile -beagleOutputToTrityper,beagleOutputToTrityper,imputeWithBeagle diff --git a/modules/compute/demo/debugFolding/inputdir/workflow.csv b/modules/compute/demo/debugFolding/inputdir/workflow.csv deleted file mode 100644 index 278ce852a6..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/workflow.csv +++ /dev/null @@ -1,31 +0,0 @@ -name,protocol_name,PreviousSteps_name -Fastqc,Fastqc, -BwaAlignLeft,BwaAlignLeft, -BwaAlignRight,BwaAlignRight, -BwaSampe,BwaSampe,"BwaAlignLeft, BwaAlignRight" -SamToBam,SamToBam,BwaSampe -SamSort,SamSort,SamToBam -PicardQC,PicardQC,SamSort -Markduplicates,Markduplicates,SamSort -RealignTargetCreator,RealignTargetCreator,Markduplicates -Realign,Realign,RealignTargetCreator -Fixmates,Fixmates,Realign -CovariatesBefore,CovariatesBefore,Fixmates -Recalibrate,Recalibrate,"Fixmates, CovariatesBefore" -SamSortRecal,SamSortRecal,Recalibrate -CovariatesAfter,CovariatesAfter,SamSortRecal -AnalyzeCovariates,AnalyzeCovariates,"CovariatesBefore, CovariatesAfter" -MergeBam,MergeBam,SamSortRecal -PicardQCrecal,PicardQCrecal,MergeBam -Coverage,Coverage,MergeBam -CoverageGATK,CoverageGATK,MergeBam -IndelGenotyper,IndelGenotyper,MergeBam -FilterIndels,FilterIndels,IndelGenotyper -UnifiedGenotyper,UnifiedGenotyper,MergeBam -MakeIndelMask,MakeIndelMask,FilterIndels -GenomicAnnotator,GenomicAnnotator,UnifiedGenotyper -VariantAnnotator,VariantAnnotator,GenomicAnnotator -VcfToTable,VcfToTable,VariantAnnotator -ConcordanceCheck,ConcordanceCheck,"MergeBam, UnifiedGenotyper" -QCReport,QCReport,"PicardQCrecal, Markduplicates, ConcordanceCheck, Coverage, VcfToTable" -CopyToResultsDir,CopyToResultsDir,"Fastqc, MergeBam, PicardQCrecal, VariantAnnotator, VcfToTable, ConcordanceCheck, QCReport" \ No newline at end of file diff --git a/modules/compute/demo/debugFolding/inputdir/worksheet.csv b/modules/compute/demo/debugFolding/inputdir/worksheet.csv deleted file mode 100644 index 918428874c..0000000000 --- a/modules/compute/demo/debugFolding/inputdir/worksheet.csv +++ /dev/null @@ -1,9 +0,0 @@ -0,internalSampleID,externalSampleID,project,contact,validationLog,labStatusPhase,labStatusComments,lastUpDate,sequencingStartDate,sequencer,run,flowcell,lane,barcodeMenu,seqType,prepKit,capturingKit,arrayFile,arrayID,GAF_QC_Name,GAF_QC_Date,GAF_QC_Status,GCC_Analysis,GCC_QC_Name,GCC_QC_Date,GCC_QC_Status,TargetDateShipment,DataShippedDate,DataShippedTo,DataShippedBy,Comments,barcode,barcodeType -,1085,1_D01_1683_RF4,SCA_B_lane6_testcompute4,"Dineke Verbeek ",,"Finished Successfully","Processing both per lane and merged!",,121010,SN163,0477,AD1C6EACXX,6,"GAF 01 -AGAGAT",PE,NEB,SureSelect_All_Exon_50MB_v4,GenomeStudio_SCA_Okt2012,1,Pieter,20121021,Passed,Yes,,,,,,,,,AGAGAT,GAF -,1086,2_D01_1640_RF4,SCA_B_lane6_testcompute4,"Dineke Verbeek ",,"Finished Successfully","Processing both per lane and merged!",,121010,SN163,0477,AD1C6EACXX,6,"GAF 03 -TCAGTT",PE,NEB,SureSelect_All_Exon_50MB_v4,GenomeStudio_SCA_Okt2012,3,Pieter,20121021,Passed,Yes,,,,,,,,,TCAGTT,GAF -,1087,3_D96_0268_RF14,SCA_B_lane6_testcompute4,"Dineke Verbeek ",,"Finished Successfully","Processing both per lane and merged!",,121010,SN163,0477,AD1C6EACXX,6,"GAF 06 -CAACCT",PE,NEB,SureSelect_All_Exon_50MB_v4,,,Pieter,20121021,Passed,Yes,,,,,,,,,CAACCT,GAF -,1088,4_D96_0264_RF14,SCA_B_lane6_testcompute4,"Dineke Verbeek ",,"Finished Successfully","Processing both per lane and merged!",,121010,SN163,0477,AD1C6EACXX,6,"GAF 12 -GGAACT",PE,NEB,SureSelect_All_Exon_50MB_v4,,,Pieter,20121021,Passed,Yes,,,,,,,,,GGAACT,GAF \ No newline at end of file diff --git a/modules/compute/demo/helloWorld/parameters.csv b/modules/compute/demo/helloWorld/parameters.csv deleted file mode 100644 index d5c267d516..0000000000 --- a/modules/compute/demo/helloWorld/parameters.csv +++ /dev/null @@ -1,5 +0,0 @@ -Name, defaultValue, description, dataType, hasOne_name -guest, , , , -party, wedding, , , -organizer, , , , -group, , , , organizer \ No newline at end of file diff --git a/modules/compute/demo/helloWorld/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/helloWorld/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/helloWorld/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/helloWorld/protocols/GuestInvitation.ftl b/modules/compute/demo/helloWorld/protocols/GuestInvitation.ftl deleted file mode 100644 index 4d55adf9f6..0000000000 --- a/modules/compute/demo/helloWorld/protocols/GuestInvitation.ftl +++ /dev/null @@ -1,2 +0,0 @@ -echo "Hello ${guest}," -echo "We invite you for our ${party}." \ No newline at end of file diff --git a/modules/compute/demo/helloWorld/protocols/OrganizerInvitation.ftl b/modules/compute/demo/helloWorld/protocols/OrganizerInvitation.ftl deleted file mode 100644 index 2078a5d39a..0000000000 --- a/modules/compute/demo/helloWorld/protocols/OrganizerInvitation.ftl +++ /dev/null @@ -1,9 +0,0 @@ -#FOREACH group - -echo "Dear ${organizer}," -echo "Please organize activities for the ${group} group." -echo "List of guests:" -<#list guest as g> - echo "${g}" - - diff --git a/modules/compute/demo/helloWorld/workflow.csv b/modules/compute/demo/helloWorld/workflow.csv deleted file mode 100644 index ae737660f7..0000000000 --- a/modules/compute/demo/helloWorld/workflow.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -GuestInvitationStep, GuestInvitation, -OrganizerInvitationStep, OrganizerInvitation, GuestInvitationStep \ No newline at end of file diff --git a/modules/compute/demo/helloWorld/worksheet.csv b/modules/compute/demo/helloWorld/worksheet.csv deleted file mode 100644 index 41d68adaea..0000000000 --- a/modules/compute/demo/helloWorld/worksheet.csv +++ /dev/null @@ -1,6 +0,0 @@ -guest, group, organizer -Charly, child, Oscar -Cindy, child, Oscar -Abel, adult, Otto -Adam, adult, Otto -Adri, adult, Otto \ No newline at end of file diff --git a/modules/compute/demo/helloWorld_debugDependencies/parameters.csv b/modules/compute/demo/helloWorld_debugDependencies/parameters.csv deleted file mode 100644 index d5c267d516..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/parameters.csv +++ /dev/null @@ -1,5 +0,0 @@ -Name, defaultValue, description, dataType, hasOne_name -guest, , , , -party, wedding, , , -organizer, , , , -group, , , , organizer \ No newline at end of file diff --git a/modules/compute/demo/helloWorld_debugDependencies/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/helloWorld_debugDependencies/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/helloWorld_debugDependencies/protocols/Footer.ftl b/modules/compute/demo/helloWorld_debugDependencies/protocols/Footer.ftl deleted file mode 100644 index 7e17f56898..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/protocols/Footer.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty footer \ No newline at end of file diff --git a/modules/compute/demo/helloWorld_debugDependencies/protocols/GuestInvitation.ftl b/modules/compute/demo/helloWorld_debugDependencies/protocols/GuestInvitation.ftl deleted file mode 100644 index 4d55adf9f6..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/protocols/GuestInvitation.ftl +++ /dev/null @@ -1,2 +0,0 @@ -echo "Hello ${guest}," -echo "We invite you for our ${party}." \ No newline at end of file diff --git a/modules/compute/demo/helloWorld_debugDependencies/protocols/Header.ftl b/modules/compute/demo/helloWorld_debugDependencies/protocols/Header.ftl deleted file mode 100644 index 0d9b0b2514..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/protocols/Header.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty header diff --git a/modules/compute/demo/helloWorld_debugDependencies/protocols/OrganizerInvitation.ftl b/modules/compute/demo/helloWorld_debugDependencies/protocols/OrganizerInvitation.ftl deleted file mode 100644 index 66a6545375..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/protocols/OrganizerInvitation.ftl +++ /dev/null @@ -1,9 +0,0 @@ -#FOREACH group, kolom - -echo "Dear ${organizer}," -echo "Please organize activities for the ${group} group." -echo "List of guests:" -<#list guest as g> - echo "${g}" - - diff --git a/modules/compute/demo/helloWorld_debugDependencies/workflow.csv b/modules/compute/demo/helloWorld_debugDependencies/workflow.csv deleted file mode 100644 index ae737660f7..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/workflow.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -GuestInvitationStep, GuestInvitation, -OrganizerInvitationStep, OrganizerInvitation, GuestInvitationStep \ No newline at end of file diff --git a/modules/compute/demo/helloWorld_debugDependencies/worksheet.csv b/modules/compute/demo/helloWorld_debugDependencies/worksheet.csv deleted file mode 100644 index c808133395..0000000000 --- a/modules/compute/demo/helloWorld_debugDependencies/worksheet.csv +++ /dev/null @@ -1,7 +0,0 @@ -guest, group, organizer, kolom -Charly, child, Oscar, a -Charly, child, Oscar, b -Cindy, child, Oscar, a -Abel, adult, Otto, d -Adam, adult, Otto, e -Adri, adult, Otto, f \ No newline at end of file diff --git a/modules/compute/demo/llrp/llrp_parameters.csv b/modules/compute/demo/llrp/llrp_parameters.csv deleted file mode 100644 index 39304da91c..0000000000 --- a/modules/compute/demo/llrp/llrp_parameters.csv +++ /dev/null @@ -1,11 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -root,$WORKDIR,Your root directory containing tools + data,, -bashAPI,xqtl.org/api/bash,,, -plink,plink,,, -workDir,${root}/workdir,,, -geno,${workDir}/llrp_geno,,, -pedFile,${geno}.ped,,, -mapFile,${geno}.map,,, -phenoInputFile,${workDir}/llrp_pheno_${pheno}.txt,,, -phenoResultFile,${workDir}/results_for_${pheno},,, -token,theToken,,, \ No newline at end of file diff --git a/modules/compute/demo/llrp/llrp_workflow.csv b/modules/compute/demo/llrp/llrp_workflow.csv deleted file mode 100644 index 176f0c4b99..0000000000 --- a/modules/compute/demo/llrp/llrp_workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -1_PlinkPhenotypeAnalysis, 1_PlinkPhenotypeAnalysis, \ No newline at end of file diff --git a/modules/compute/demo/llrp/llrp_worksheet.csv b/modules/compute/demo/llrp/llrp_worksheet.csv deleted file mode 100644 index bc7e3264da..0000000000 --- a/modules/compute/demo/llrp/llrp_worksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -pheno -Health19 \ No newline at end of file diff --git a/modules/compute/demo/llrp/protocols/1_PlinkPhenotypeAnalysis.ftl b/modules/compute/demo/llrp/protocols/1_PlinkPhenotypeAnalysis.ftl deleted file mode 100644 index f7c31bd55c..0000000000 --- a/modules/compute/demo/llrp/protocols/1_PlinkPhenotypeAnalysis.ftl +++ /dev/null @@ -1,14 +0,0 @@ -#MOLGENIS walltime=00:45:00 mem=2GB nodes=1 cores=2 - -source ${bashAPI} - -login ${token} - -getFile ${pedFile} -getFile ${mapFile} -getFile ${phenoInputFile} - -#run Plink -${plink} --noweb --file ${geno} --pheno ${phenoInputFile} --assoc --maf 0.05 --hwe -0.001 --1 --allow-no-sex --out ${phenoResultFile} - -putFile ${phenoResultFile} \ No newline at end of file diff --git a/modules/compute/demo/llrp/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/llrp/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/llrp/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/llrp/protocols/Footer.ftl b/modules/compute/demo/llrp/protocols/Footer.ftl deleted file mode 100644 index 7e17f56898..0000000000 --- a/modules/compute/demo/llrp/protocols/Footer.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty footer \ No newline at end of file diff --git a/modules/compute/demo/llrp/protocols/Header.ftl b/modules/compute/demo/llrp/protocols/Header.ftl deleted file mode 100644 index 0d9b0b2514..0000000000 --- a/modules/compute/demo/llrp/protocols/Header.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty header diff --git a/modules/compute/demo/lspilot1/lspilot1_commands b/modules/compute/demo/lspilot1/lspilot1_commands deleted file mode 100644 index bc67fde53f..0000000000 --- a/modules/compute/demo/lspilot1/lspilot1_commands +++ /dev/null @@ -1,12 +0,0 @@ -1. plink --noweb --bed GvNL_good_samples.bed --bim GvNL_good_samples.bim --fam GvNL_good_samples.fam --remove GvNL_suspicious.txt --make-bed --out out1_1 -2. plink --noweb --silent --bfile out1_1 --update-ids GvNL_family_update.txt --make-bed --out out2_1 -3. plink --noweb --bfile out2_1 --update-parents GvNL_parents_update.txt --make-bed --out out3_1 -4. plink --noweb --bfile out3_1 --check-sex --make-bed --out out4_1 -5. does not work: plink --noweb --silent --bfile out3_1 --update-sex out4_1.sexcheck --make-bed --out out5_1 -6. plink --noweb --bfile out4_1 --missing --out out6_1 -7. plink --noweb --bfile out4_1 --het --out out7_1 -9. sh run.sh -A. plink --noweb --bfile out4_1 --remove out9_1.txt --out outA_1 -B. plink --noweb --bfile out4_1 --indep-pairwise 50 5 0.2 --out outB_1 -C. plink --noweb --bfile out4 --extract outB.prune.in --genome --out outC -D. plink --noweb --bfile out4 --me 0.05 0.1 --make-bed --out outD \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/lspilot1_parameters_cluster.csv b/modules/compute/demo/lspilot1/lspilot1_parameters_cluster.csv deleted file mode 100644 index dad5771fb5..0000000000 --- a/modules/compute/demo/lspilot1/lspilot1_parameters_cluster.csv +++ /dev/null @@ -1,33 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -root,$WORKDIR,Your root directory containing tools + data,, -scriptDir,${root}/tools/scripts,, -mem,2GB,,, -nodes,1,,, -cores,1,,, -workDir,~/development/lspilot1/data,,, -plink,plink,,, -badSampleFile,${workDir}/GvNL_suspicious.txt,,, -filePrefix,${workDir}/${target},,, -bedFile,${filePrefix}.bed,,, -bimFile,${filePrefix}.bim,,, -famFile,${filePrefix}.fam,,, -filehandleRemoveString,${filePrefix}.out1,,, -familyUpdateFile,${workDir}/GvNL_family_update.txt,,, -filehandleUpdateIdsString,${filePrefix}.out2,,, -parentsUpdateFile,${workDir}/GvNL_parents_update.txt,,, -filehandleUpdateParentsString,${filePrefix}.out3,,, -filehandleSexCheckString,${filePrefix}.out4,,, -filehandleUpdateSexString,${filePrefix}.out4,,, -filehandleMissingString,${filePrefix}.out6,,, -filehandleHeterozygosityString,${filePrefix}.out7,,, -R,/target/gpfs2/gcc/tools/R/bin/R,,, -filehandleFilterString,${filePrefix}.out9,,, -filehandleRemoveSampleString,${filePrefix}.outA,,, -snpWindowN,50,,, -snpIntervalM,5,,, -rSquaredThreshold,0.2,,, -filehandlePairwiseString,${filePrefix}.outB,,, -filehandleGenomeString,${filePrefix}.outC,,, -familyError,0.05,,, -snpError,0.1,,, -filehandleMendelString,${filePrefix}.outD,,, \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/lspilot1_parameters_grid.csv b/modules/compute/demo/lspilot1/lspilot1_parameters_grid.csv deleted file mode 100644 index e2666b23e6..0000000000 --- a/modules/compute/demo/lspilot1/lspilot1_parameters_grid.csv +++ /dev/null @@ -1,33 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -root,$WORKDIR/lspilot1,Your root directory containing tools + data,, -workDir,${root},,, -mem,2GB,,, -cores,1,,, -nodes,1,,, -plink,plink,,, -badSampleFile,${workDir}/GvNL_suspicious.txt,,, -filePrefix,${workDir}/${target},,, -bedFile,${filePrefix}.bed,,, -bimFile,${filePrefix}.bim,,, -famFile,${filePrefix}.fam,,, -filehandleRemoveString,${filePrefix}.out1,,, -familyUpdateFile,${workDir}/GvNL_family_update.txt,,, -filehandleUpdateIdsString,${filePrefix}.out2,,, -parentsUpdateFile,${workDir}/GvNL_parents_update.txt,,, -filehandleUpdateParentsString,${filePrefix}.out3,,, -filehandleSexCheckString,${filePrefix}.out4,,, -filehandleUpdateSexString,${filePrefix}.out4,,, -filehandleMissingString,${filePrefix}.out6,,, -filehandleHeterozygosityString,${filePrefix}.out7,,, -R,/target/gpfs2/gcc/tools/R/bin/R,,, -filehandleFilterString,${filePrefix}.out9,,, -filehandleRemoveSampleString,${filePrefix}.outA,,, -snpWindowN,50,,, -snpIntervalM,5,,, -rSquaredThreshold,0.2,,, -filehandlePairwiseString,${filePrefix}.outB,,, -filehandleGenomeString,${filePrefix}.outC,,, -familyError,0.05,,, -snpError,0.1,,, -filehandleMendelString,${filePrefix}.outD,,, - diff --git a/modules/compute/demo/lspilot1/lspilot1_workflow_cluster.csv b/modules/compute/demo/lspilot1/lspilot1_workflow_cluster.csv deleted file mode 100644 index 2d880a3b14..0000000000 --- a/modules/compute/demo/lspilot1/lspilot1_workflow_cluster.csv +++ /dev/null @@ -1,14 +0,0 @@ -name,protocol_name,PreviousSteps_name -1_RemoveBadSamples, 1_RemoveBadSamples, -2_UpdateFamilyIDs, 2_UpdateFamilyIDs, 1_RemoveBadSamples -3_UpdateParents, 3_UpdateParents, 2_UpdateFamilyIDs -4_SexCheck, 4_SexCheck, 3_UpdateParents -5_UpdateSex, 5_UpdateSex, 4_SexCheck -6_Missingness, 6_Missingness, 5_UpdateSex -7_Heterozygosity, 7_Heterozygosity, 6_Missingness -8_Join, 8_Join, 7_Heterozygosity -9_HeterozygosityFilter, 9_HeterozygosityFilter, 8_Join -A_RemoveSamples, A_RemoveSamples, 9_HeterozygosityFilter -B_SNPPruning, B_SNPPruning, A_RemoveSamples -C_PairwiseIBS, C_PairwiseIBS, B_SNPPruning -D_MendelErrorRate, D_MendelErrorRate, C_PairwiseIBS diff --git a/modules/compute/demo/lspilot1/lspilot1_workflow_grid.csv b/modules/compute/demo/lspilot1/lspilot1_workflow_grid.csv deleted file mode 100644 index d2d09c6b2e..0000000000 --- a/modules/compute/demo/lspilot1/lspilot1_workflow_grid.csv +++ /dev/null @@ -1,7 +0,0 @@ -name,protocol_name,PreviousSteps_name -1_RemoveBadSamples,1_RemoveBadSamples -2_UpdateFamilyIDs,2_UpdateFamilyIDs,1_RemoveBadSamples -3_UpdateParents,3_UpdateParents,2_UpdateFamilyIDs -4_SexCheck,4_SexCheck,3_UpdateParents -6_Missingness,6_Missingness,4_SexCheck -7_Heterozygosity,7_Heterozygosity,6_Missingness \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/lspilot1_worksheet.csv b/modules/compute/demo/lspilot1/lspilot1_worksheet.csv deleted file mode 100644 index 5bf7ef95cb..0000000000 --- a/modules/compute/demo/lspilot1/lspilot1_worksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -target -GvNL_good_samples \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/1_RemoveBadSamples.ftl b/modules/compute/demo/lspilot1/protocols/1_RemoveBadSamples.ftl deleted file mode 100644 index 6024456125..0000000000 --- a/modules/compute/demo/lspilot1/protocols/1_RemoveBadSamples.ftl +++ /dev/null @@ -1,17 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${bedFile} -getFile ${bimFile} -getFile ${famFile} -getFile ${badSampleFile} - -${plink} --noweb --bed ${bedFile} --bim ${bimFile} --fam ${famFile} --remove ${badSampleFile} --make-bed --out ${filehandleRemoveString} - -putFile ${filehandleRemoveString}.bed -putFile ${filehandleRemoveString}.nof -putFile ${filehandleRemoveString}.hh -putFile ${filehandleRemoveString}.fam -putFile ${filehandleRemoveString}.bim -putFile ${filehandleRemoveString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/2_UpdateFamilyIDs.ftl b/modules/compute/demo/lspilot1/protocols/2_UpdateFamilyIDs.ftl deleted file mode 100644 index b59e2f29f5..0000000000 --- a/modules/compute/demo/lspilot1/protocols/2_UpdateFamilyIDs.ftl +++ /dev/null @@ -1,20 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleRemoveString}.bed -getFile ${filehandleRemoveString}.nof -getFile ${filehandleRemoveString}.hh -getFile ${filehandleRemoveString}.fam -getFile ${filehandleRemoveString}.bim -getFile ${filehandleRemoveString}.nosex -getFile ${familyUpdateFile} - -${plink} --noweb --bfile ${filehandleRemoveString} --update-ids ${familyUpdateFile} --make-bed --out ${filehandleUpdateIdsString} - -putFile ${filehandleUpdateIdsString}.bed -putFile ${filehandleUpdateIdsString}.nof -putFile ${filehandleUpdateIdsString}.hh -putFile ${filehandleUpdateIdsString}.fam -putFile ${filehandleUpdateIdsString}.bim -putFile ${filehandleUpdateIdsString}.nosex diff --git a/modules/compute/demo/lspilot1/protocols/3_UpdateParents.ftl b/modules/compute/demo/lspilot1/protocols/3_UpdateParents.ftl deleted file mode 100644 index ccd66ae488..0000000000 --- a/modules/compute/demo/lspilot1/protocols/3_UpdateParents.ftl +++ /dev/null @@ -1,20 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${parentsUpdateFile} -getFile ${filehandleUpdateIdsString}.bed -getFile ${filehandleUpdateIdsString}.nof -getFile ${filehandleUpdateIdsString}.hh -getFile ${filehandleUpdateIdsString}.fam -getFile ${filehandleUpdateIdsString}.bim -getFile ${filehandleUpdateIdsString}.nosex - -${plink} --noweb --bfile ${filehandleUpdateIdsString} --update-parents ${parentsUpdateFile} --make-bed --out ${filehandleUpdateParentsString} - -putFile ${filehandleUpdateParentsString}.bed -putFile ${filehandleUpdateParentsString}.nof -putFile ${filehandleUpdateParentsString}.hh -putFile ${filehandleUpdateParentsString}.fam -putFile ${filehandleUpdateParentsString}.bim -putFile ${filehandleUpdateParentsString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/4_SexCheck.ftl b/modules/compute/demo/lspilot1/protocols/4_SexCheck.ftl deleted file mode 100644 index 9492f957aa..0000000000 --- a/modules/compute/demo/lspilot1/protocols/4_SexCheck.ftl +++ /dev/null @@ -1,22 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateParentsString}.bed -getFile ${filehandleUpdateParentsString}.nof -getFile ${filehandleUpdateParentsString}.hh -getFile ${filehandleUpdateParentsString}.fam -getFile ${filehandleUpdateParentsString}.bim -getFile ${filehandleUpdateParentsString}.nosex - -${plink} --noweb --bfile ${filehandleUpdateParentsString} --check-sex --make-bed --out ${filehandleSexCheckString} - -putFile ${filehandleSexCheckString}.bed -putFile ${filehandleSexCheckString}.sexcheck -putFile ${filehandleSexCheckString}.nof -putFile ${filehandleSexCheckString}.hh -putFile ${filehandleSexCheckString}.fam -putFile ${filehandleSexCheckString}.bim -putFile ${filehandleSexCheckString}.nosex - - \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/5_UpdateSex.ftl b/modules/compute/demo/lspilot1/protocols/5_UpdateSex.ftl deleted file mode 100644 index e9d1966981..0000000000 --- a/modules/compute/demo/lspilot1/protocols/5_UpdateSex.ftl +++ /dev/null @@ -1,13 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -#module load plink - -#This step should automatically correct the sexes of the samples. -#Officially we'd run the following command, however, the UpdateSexFile is missing. Therefore, this step (5) fails. -#${plink} --noweb --silent --bfile ${filehandleUpdateParentsString} --update-sex ${filehandleSexCheckString} --make-bed --out ${filehandleUpdateSexString} - -#To fix this, one can combine steps 4 and 5 by the following command: -#/target/gpfs2/gcc/tools/plink-1.07-x86_64/plink --noweb --silent --bfile out3 --impute-sex --make-bed --out out5 - -#However, the sexes are predicted wrongly in most cases (checked manually). Therefore, we skip this step. - \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/6_Missingness.ftl b/modules/compute/demo/lspilot1/protocols/6_Missingness.ftl deleted file mode 100644 index 5a9f9208a3..0000000000 --- a/modules/compute/demo/lspilot1/protocols/6_Missingness.ftl +++ /dev/null @@ -1,19 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateSexString}.bed -getFile ${filehandleUpdateSexString}.sexcheck -getFile ${filehandleUpdateSexString}.nof -getFile ${filehandleUpdateSexString}.hh -getFile ${filehandleUpdateSexString}.fam -getFile ${filehandleUpdateSexString}.bim -getFile ${filehandleUpdateSexString}.nosex - -${plink} --noweb --bfile ${filehandleUpdateSexString} --missing --out ${filehandleMissingString} - -putFile ${filehandleMissingString}.hh -putFile ${filehandleMissingString}.imiss -putFile ${filehandleMissingString}.lmiss -putFile ${filehandleMissingString}.nof -putFile ${filehandleMissingString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/7_Heterozygosity.ftl b/modules/compute/demo/lspilot1/protocols/7_Heterozygosity.ftl deleted file mode 100644 index 7525738f88..0000000000 --- a/modules/compute/demo/lspilot1/protocols/7_Heterozygosity.ftl +++ /dev/null @@ -1,18 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateSexString}.bed -getFile ${filehandleUpdateSexString}.sexcheck -getFile ${filehandleUpdateSexString}.nof -getFile ${filehandleUpdateSexString}.hh -getFile ${filehandleUpdateSexString}.fam -getFile ${filehandleUpdateSexString}.bim -getFile ${filehandleUpdateSexString}.nosex - -${plink} --noweb --bfile ${filehandleUpdateSexString} --het --out ${filehandleHeterozygosityString} - -putFile ${filehandleHeterozygosityString}.het -putFile ${filehandleHeterozygosityString}.nof -putFile ${filehandleHeterozygosityString}.hh -putFile ${filehandleHeterozygosityString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/8_Join.ftl b/modules/compute/demo/lspilot1/protocols/8_Join.ftl deleted file mode 100644 index df286d1ba6..0000000000 --- a/modules/compute/demo/lspilot1/protocols/8_Join.ftl +++ /dev/null @@ -1,4 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -# This step will be solved in the R-script of step 9. -<#noparse>#join -1 "FID" -2 "FID" ${filehandleMissingString} ${filehandleHeterozygosityString} > ${filehandleJoinString} \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/9_HeterozygosityFilter.ftl b/modules/compute/demo/lspilot1/protocols/9_HeterozygosityFilter.ftl deleted file mode 100644 index a7e6a9b6fe..0000000000 --- a/modules/compute/demo/lspilot1/protocols/9_HeterozygosityFilter.ftl +++ /dev/null @@ -1,21 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -getFile ${filehandleHeterozygosityString}.het -getFile ${filehandleMissingString}.imiss - -#Run R -${R} --slave --vanilla < mean(het$"HET_RATE")+3*sd(het$"HET_RATE"))); -het_fail$"HET_DST" = (het_fail$"HET_RATE"-mean(het$"HET_RATE"))/sd(het$"HET_RATE"); - -write.table(het_fail, "${filehandleFilterString}", row.names=FALSE); - -RSCRIPT - -putFile ${filehandleFilterString} \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/A_RemoveSamples.ftl b/modules/compute/demo/lspilot1/protocols/A_RemoveSamples.ftl deleted file mode 100644 index 53fcf0b4c6..0000000000 --- a/modules/compute/demo/lspilot1/protocols/A_RemoveSamples.ftl +++ /dev/null @@ -1,19 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateSexString}.bed -getFile ${filehandleUpdateSexString}.bim -getFile ${filehandleUpdateSexString}.fam -getFile ${filehandleUpdateSexString}.hh -getFile ${filehandleUpdateSexString}.nof -getFile ${filehandleUpdateSexString}.nosex -getFile ${filehandleUpdateSexString}.sexcheck -getFile ${filehandleFilterString} - -${plink} --noweb --silent --bfile ${filehandleUpdateSexString} --remove ${filehandleFilterString} --out ${filehandleRemoveSampleString} - -putFile ${filehandleRemoveSampleString}.hh -putFile ${filehandleRemoveSampleString}.log -putFile ${filehandleRemoveSampleString}.nof -putFile ${filehandleRemoveSampleString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/B_SNPPruning.ftl b/modules/compute/demo/lspilot1/protocols/B_SNPPruning.ftl deleted file mode 100644 index 14a6e25513..0000000000 --- a/modules/compute/demo/lspilot1/protocols/B_SNPPruning.ftl +++ /dev/null @@ -1,20 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateSexString}.bed -getFile ${filehandleUpdateSexString}.bim -getFile ${filehandleUpdateSexString}.fam -getFile ${filehandleUpdateSexString}.hh -getFile ${filehandleUpdateSexString}.nof -getFile ${filehandleUpdateSexString}.nosex -getFile ${filehandleUpdateSexString}.sexcheck - -${plink} --noweb --silent --bfile ${filehandleUpdateSexString} --indep-pairwise ${snpWindowN} ${snpIntervalM} ${rSquaredThreshold} --out ${filehandlePairwiseString} - -putFile ${filehandlePairwiseString}.hh -putFile ${filehandlePairwiseString}.nof -putFile ${filehandlePairwiseString}.prune.in -putFile ${filehandlePairwiseString}.log -putFile ${filehandlePairwiseString}.nosex -putFile ${filehandlePairwiseString}.prune.out \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/C_PairwiseIBS.ftl b/modules/compute/demo/lspilot1/protocols/C_PairwiseIBS.ftl deleted file mode 100644 index 69e9a0c341..0000000000 --- a/modules/compute/demo/lspilot1/protocols/C_PairwiseIBS.ftl +++ /dev/null @@ -1,19 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateSexString}.bed -getFile ${filehandleUpdateSexString}.sexcheck -getFile ${filehandleUpdateSexString}.nof -getFile ${filehandleUpdateSexString}.hh -getFile ${filehandleUpdateSexString}.fam -getFile ${filehandleUpdateSexString}.bim -getFile ${filehandleUpdateSexString}.nosex -getFile ${filehandlePairwiseString}.prune.in - -${plink} --noweb --silent --bfile ${filehandleUpdateSexString} --extract ${filehandlePairwiseString}.prune.in --genome --out ${filehandleGenomeString} - -putFile ${filehandleGenomeString}.genome -putFile ${filehandleGenomeString}.hh -putFile ${filehandleGenomeString}.log -putFile ${filehandleGenomeString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/lspilot1/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/lspilot1/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/lspilot1/protocols/D_MendelErrorRate.ftl b/modules/compute/demo/lspilot1/protocols/D_MendelErrorRate.ftl deleted file mode 100644 index 3d4025d9fc..0000000000 --- a/modules/compute/demo/lspilot1/protocols/D_MendelErrorRate.ftl +++ /dev/null @@ -1,21 +0,0 @@ -#MOLGENIS walltime=00:45:00 - -module load plink - -getFile ${filehandleUpdateSexString}.bed -getFile ${filehandleUpdateSexString}.sexcheck -getFile ${filehandleUpdateSexString}.nof -getFile ${filehandleUpdateSexString}.hh -getFile ${filehandleUpdateSexString}.fam -getFile ${filehandleUpdateSexString}.bim -getFile ${filehandleUpdateSexString}.nosex - -${plink} --noweb --silent --bfile ${filehandleUpdateSexString} --me ${familyError} ${snpError} --make-bed --out ${filehandleMendelString} - -putFile ${filehandleMendelString}.bed -putFile ${filehandleMendelString}.bim -putFile ${filehandleMendelString}.fam -putFile ${filehandleMendelString}.hh -putFile ${filehandleMendelString}.log -putFile ${filehandleMendelString}.nof -putFile ${filehandleMendelString}.nosex \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/Footer.ftl b/modules/compute/demo/lspilot1/protocols/Footer.ftl deleted file mode 100644 index 7e17f56898..0000000000 --- a/modules/compute/demo/lspilot1/protocols/Footer.ftl +++ /dev/null @@ -1 +0,0 @@ -# Empty footer \ No newline at end of file diff --git a/modules/compute/demo/lspilot1/protocols/Header.ftl b/modules/compute/demo/lspilot1/protocols/Header.ftl deleted file mode 100644 index 5942dc1c68..0000000000 --- a/modules/compute/demo/lspilot1/protocols/Header.ftl +++ /dev/null @@ -1,8 +0,0 @@ -# Header - begin - -# Configures the GCC bash environment -. ${root}/gcc.bashrc - -source ${scriptDir}/dataTransferCluster.sh - -# Header - end diff --git a/modules/compute/demo/mach_minimach/minimacStage3/exampleWorksheet.csv b/modules/compute/demo/mach_minimach/minimacStage3/exampleWorksheet.csv deleted file mode 100644 index 8881fd0b4d..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/exampleWorksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,studyInputDir,referencePanel,imputationResultDir,imputationPipeline,genomeBuild,chr,autostart -1240Blood_b37,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood_b37/,gonl_release3.1,${root}/home/fvandijk/minimac/test2,minimac,b37,20,TRUE diff --git a/modules/compute/demo/mach_minimach/minimacStage3/parameters.csv b/modules/compute/demo/mach_minimach/minimacStage3/parameters.csv deleted file mode 100644 index 1fa056cfe5..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/parameters.csv +++ /dev/null @@ -1,97 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,default,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc/,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -resdir,${root}/resources,,, -#,,,, -tempdir,${imputationResultDir}/tmp/,,, -plink,${tooldir}/plink-${plinkversion}/plink,,, -plinkversion,1.07-x86_64,,, -plinkseqBin,${tooldir}/plink-${plinkseqversion}/plink108,,, -plinkseqversion,1.08,,, -projectPhasingJobsDir,${McScripts}/../phasing/,,, -projectImputationJobsDir,${McScripts}/../imputation/,,, -projectPhasingJobsDirTarGz,${McScripts}/../phasing.tar.gz,,, -projectImputationJobsDirTarGz,${McScripts}/../imputation.tar.gz,,, -projectTempDir,${tempdir}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyInputPedMapChr,${studyInputDir}/chr${chr},,, -studyPedMapChrDir,${studyPedMapDir}/chr${chr}/,,, -studyPedMapChr,${studyPedMapChrDir}/chr${chr},,, -studyTriTyperChrTempDir,${projectTempDir}/StudyTriTyper/~chr${chr}/,end with slash,, -studyTriTyperChrDir,${projectTempDir}/StudyTriTyper/chr${chr}/,end with slash,, -preparedStudyTempDir,${projectTempDir}/preparedStudy/~${chr}/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/${chr}/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,gtool,,, -#gtoolBin,${tooldir}/gtool_${gtoolBinversion}/gtool,,, -gtoolBinversion,v0.7.5_x86_64,,, -referenceFolder,${resdir}/imputationReference/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/Chr${chr}/,end with slash,, -pythonversion,2.7.3,,, -javaversion,1.6.0_33,,, -imputationToolJar,${tooldir}/ImputationTool-${imputationToolJarversion}/ImputationTool.jar,,, -imputationToolJarversion,20120912,,, -imputationToolLibDir,${tooldir}/ImputationTool-${imputationToolJarversion}/lib/,,, -imputationToolGeneticaLibrariesJar,${imputationToolLibDir}/GeneticaLibraries.jar,,, -imputationToolJsciCoreJar,${imputationToolLibDir}/jsci-core-1.1.jar,,, -convertB36ChrTempDir,${projectTempDir}/b36conversion/,,, -convertB36ChrHg19Bed,${convertB36ChrTempDir}/chr_${chr}Hg19.bed,,, -convertB36unmapped,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -convertB36unmappedSNPs,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -b36conversionPedMapResultDir,${imputationResultDir}/b36PedMap/,,, -liftOverUcscBin,${tooldir}/liftOverUcsc-${liftOverUcscBinversion}/liftOver,,, -liftOverUcscBinversion,20120905,,, -convertB36ChrHg18Bed,${convertB36ChrTempDir}/chr_${chr}Hg18.bed,,, -liftoverDir,${resdir}/liftover/,,, -hg19ToHg18chainfile,${liftoverDir}/hg19ToHg18.over.chain,,, -project,,,,"imputationResultDir,studyInputDir,referencePanel,imputationPipeline" -expandWorksheetJar,${tooldir}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}.jar,,, -expandWorksheetJarversion,V1.1,,, -concatWorksheetsJar,${tooldir}/ConcatWorksheets${concatWorksheetsJarversion}/ConcatWorksheets${concatWorksheetsJarversion}.jar -concatWorksheetsJarversion,V1.0,,, -#,,,, -chr,,,, -chunkSize,2000,,, -chunkOverlap,750,,, -chunkChromosomeBin,${tooldir}/ChunkChromosome-${chunkChromosomeBinVersion}/ChunkChromosome,,, -chunkChromosomeBinVersion,2012-08-28,,, -chunk,,,, -chunkChrWorkSheet,${tempdir}/tmpChr${chr}ChunkWorksheet.csv,,, -finalChunkChrWorksheet,${tempdir}/ChunkChr${chr}Worksheet.csv,,, -tmpFinalChunkChrWorksheet,${tempdir}/~ChunkChr${chr}Worksheet.csv,,, -concattedChunkWorksheet,${McScripts}/../concattedChunkWorksheet.csv,,, -tmpConcattedChunkWorksheet,${McScripts}/../~concattedChunkWorksheet.csv,,, -studyMerlinDir,${tempdir}/studyMerlin/,,, -studyMerlinChrDir,${studyMerlinDir}/chr${chr}/,,, -studyMerlinChrMap,${studyMerlinChrDir}/chr${chr}.map,,, -studyMerlinChrDat,${studyMerlinChrDir}/chr${chr}.dat,,, -studyMerlinChrPed,${studyMerlinChrDir}/chr${chr}.ped,,, -machBin,${tooldir}/mach.${machBinversion}/executables/mach1,,, -machBinversion,1.0.18,,, -studyChunkDir,${tempdir}/studyChunks,,, -studyChunkChrDir,${studyChunkDir}/chr${chr}/,,, -phasingRounds,20,,, -phasingStates,200,,, -phasingHaplotypeSampling,5,,, -minimacOmpBin,${tooldir}/minimac-beta-${minimacVersion}/minimac-omp,,, -minimacBin,${tooldir}/minimac-beta-${minimacVersion}/minimac,,, -minimacVersion,2012.10.3,,, -referenceChrVcf,${referenceFolder}/${referencePanel}/vcf/chr${chr}.vcf,,, -referenceChrVcfGz,${referenceFolder}/${referencePanel}/vcf/chr${chr}.vcf.gz,,, -#,,,, -studyInputDir,,,, -referencePanel,,,, -imputationResultDir,,,, -imputationPipeline,,,, -genomeBuild,,,, -autostart,TRUE,,, diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index 15513f7867..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 0 - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Footer.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Header.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/Header.ftl deleted file mode 100644 index 32e91a79b6..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Header.ftl +++ /dev/null @@ -1,34 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#!/bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - -<#elseif scheduler == "GRID"> - - - - -<#if scheduler != "GRID"> -# Configures the GCC bash environment -. ${root}/gcc.bashrc - - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Helpers.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Macros.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/NGSHeader.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/chunkChromosome.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/chunkChromosome.ftl deleted file mode 100644 index e6d7b33280..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/chunkChromosome.ftl +++ /dev/null @@ -1,85 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${chunkChromosomeBin} -getFile ${expandWorksheetJar} - -getFile ${studyMerlinChrDat} -getFile ${McWorksheet} - -inputs "${studyMerlinChrDat}" -inputs "${McWorksheet}" - - -#!!!! -#alloutputsexist \ -# "${studyMerlinChrDir}/chunk$c-chr${chr}.dat.snps" \ -$ "${studyMerlinChrDir}/chunk$c-chr${chr}.dat" - -#Chunk chromosomes into pieces containing ~${chunkSize} markers - -cd ${studyMerlinChrDir} - -${chunkChromosomeBin} \ - -d ${studyMerlinChrDat} \ - -n ${chunkSize} \ - -o ${chunkOverlap} - -returnCode=$? - -if [ $returnCode -ne 0 ] -then - - echo -e "\nNon zero return code. Something went wrong creating the chunks\n\n" - #Return non zero return code - exit 1 - -fi - -#Create .csv file to be merged with original worksheet -echo "chunk" > ${chunkChrWorkSheet} - - -chunks=(${studyMerlinChrDir}/chunk*-chr${chr}.dat.snps) - -s=${r"${#chunks[*]}"} - -for c in `seq 1 $s` -do - echo $c >> ${chunkChrWorkSheet} - putFile ${studyMerlinChrDir}/chunk$c-chr${chr}.dat.snps - putFile ${studyMerlinChrDir}/chunk$c-chr${chr}.dat -done - - -#Merge worksheets -module load jdk/${javaversion} - -#Run Jar to create full worksheet - - -java -jar ${expandWorksheetJar} ${McWorksheet} ${tmpFinalChunkChrWorksheet} ${chunkChrWorkSheet} project ${project} chr ${chr} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${tmpFinalChunkChrWorksheet} ${finalChunkChrWorksheet} - - putFile ${finalChunkChrWorksheet} - - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/convertPedMapToTriTyper.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/convertPedMapToTriTyper.ftl deleted file mode 100644 index 62ad8ba171..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/convertPedMapToTriTyper.ftl +++ /dev/null @@ -1,61 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${imputationToolJar} -getFile ${imputationToolJsciCoreJar} -getFile ${imputationToolGeneticaLibrariesJar} - -getFile ${studyPedMapChr}.map -getFile ${studyPedMapChr}.ped - - - -inputs "${studyPedMapChr}.map" -inputs "${studyPedMapChr}.ped" -alloutputsexist "${studyTriTyperChrDir}/GenotypeMatrix.dat" \ - "${studyTriTyperChrDir}/Individuals.txt" \ - "${studyTriTyperChrDir}/PhenotypeInformation.txt" \ - "${studyTriTyperChrDir}/SNPMappings.txt" \ - "${studyTriTyperChrDir}/SNPs.txt" - - -if [ -d ${studyTriTyperChrDir} ] -then - rm -r ${studyTriTyperChrDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${studyTriTyperChrTempDir} - -java -jar ${imputationToolJar} \ - --mode pmtt \ - --in ${studyPedMapChrDir} \ - --out ${studyTriTyperChrTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${studyTriTyperChrTempDir} ${studyTriTyperChrDir} - - putFile "${studyTriTyperChrDir}/GenotypeMatrix.dat" - putFile "${studyTriTyperChrDir}/Individuals.txt" - putFile "${studyTriTyperChrDir}/PhenotypeInformation.txt" - putFile "${studyTriTyperChrDir}/SNPMappings.txt" - putFile "${studyTriTyperChrDir}/SNPs.txt" - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/convertPlinkPedMapToMerlin.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/convertPlinkPedMapToMerlin.ftl deleted file mode 100644 index 1fb7d457bc..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/convertPlinkPedMapToMerlin.ftl +++ /dev/null @@ -1,38 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${preparedStudyDir}/chr${chr}.map -getFile ${preparedStudyDir}/chr${chr}.ped -getFile ${studyPedMapChr}.ped - -inputs ${preparedStudyDir}/chr${chr}.map -inputs ${preparedStudyDir}/chr${chr}.ped -inputs ${studyPedMapChr}.ped - - -alloutputsexist \ -"${studyMerlinChrMap}" \ -"${studyMerlinChrDat}" \ -"${studyMerlinChrPed}" - -mkdir -p ${studyMerlinChrDir} - -#Conver SNP ID to chr_pos and remove 3e column to adhere to merlin -gawk ' - BEGIN {$1="CHROMOSOME";$2="MARKER";$3="POSITION";print $0} - {$2=$1":"$4;print $1,$2,$4} -' OFS="\t" ${preparedStudyDir}/chr${chr}.map > ${studyMerlinChrMap} - -gawk 'BEGIN {print "T","pheno";}{print "M",$1":"$4}' ${preparedStudyDir}/chr${chr}.map > ${studyMerlinChrDat} - -set +o posix - -#Create merlin ped from genotypes outputed by imputation tool but use fam id, sample id and phenodata from original pedmap -paste <(awk '{print $1,$2,$3,$4,$5,$6}' ${studyPedMapChr}.ped) <(awk '{for(i=7;i ${studyMerlinChrPed} - -putFile ${studyMerlinChrMap} -putFile ${studyMerlinChrDat} -putFile ${studyMerlinChrPed} - - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/mergeMinimacImputationResults.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/mergeMinimacImputationResults.ftl deleted file mode 100644 index 2ec45b2492..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/mergeMinimacImputationResults.ftl +++ /dev/null @@ -1,62 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -Fix in- and outputs later -#getFile - -#Retrieve number of chunks (list) -s=${chunk?size} - - -##Paste resulting chunk *.impuated.dose files together -cp ${studyChunkChrDir}/chunk1-chr${chr}.imputed.dose ${studyChunkChrDir}/chunk1-chr${chr}.imputed.dose.tmp - -<#assign x=chunk?size+1> - -<#if x gt 1> -for c in `seq 2 $s` -do - cut -f3- ${studyChunkChrDir}/chunk$c-chr${chr}.imputed.dose \ - > ${studyChunkChrDir}/chunk$c-chr${chr}.imputed.dose.tmp -done - - -paste \ -<#list chunk as chnk> -${studyChunkChrDir}/chunk${chnk}-chr${chr}.imputed.dose.tmp \ - -> ${imputationResultDir}/chr${chr}.imputed.merged.dose - -#Concat *.rec and *.info chunk files - -<#assign x=chunk?size+1> - -<#if x gt 1> -( cat ${studyChunkChrDir}/chunk1-chr${chr}.imputed.info <#list 2..x as chnk><#if chnk_has_next>; tail -n +2 ${studyChunkChrDir}/chunk${chnk}-chr${chr}.imputed.info ) \ ->> ${imputationResultDir}/chr${chr}.imputed.merged.info - - - -#Create *.fam file from *.imputed.dose and original ped file - -awk '{print $1}' ${studyChunkChrDir}/chunk1-chr${chr}.imputed.dose \ -| awk '{print $1,$2}' FS="->" OFS="_" > ${studyChunkChrDir}/chr${chr}_fam_sample.txt - -awk '{$7=$1"_"$2;print $7,$1,$2,$3,$4,$5,$6}' \ -${studyPedMapChr}.ped \ -> ${studyChunkChrDir}/chr${chr}.tmp.ped - -awk ' FILENAME=="${studyChunkChrDir}/chr${chr}.tmp.ped" \ -{arr[$1]=$0; next} FILENAME=="${studyChunkChrDir}/chr${chr}_fam_sample.txt" \ -{print arr[$1]} ' ${studyChunkChrDir}/chr${chr}.tmp.ped \ -${studyChunkChrDir}/chr${chr}_fam_sample.txt \ -| awk '{print $1,$2,$3,$4,$5,$6,$7}' \ -| awk '{ -if ($0 ~ /^[ ]*$/) \ - print "FamilyID_SampleID combination not found in original PED file!" > "/dev/stderr" - exit 1; \ -else - print $2,$3,$4,$5,$6,$7}' \ -> ${imputationResultDir}/chr${chr}.fam - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/minimacImputation.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/minimacImputation.ftl deleted file mode 100644 index e0b49de81b..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/minimacImputation.ftl +++ /dev/null @@ -1,61 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr,chunk - -getFile ${minimacBin} - -getFile ${referenceChrVcf} -getFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz -getFile ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps - -inputs "${referenceChrVcf}" -inputs "${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz" -inputs "${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps" - -alloutputsexist \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.dose \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.erate \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info.draft \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.rec \ -${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log - - -${minimacBin} \ - --refHaps ${referenceChrVcf} \ - --vcfReference \ - --haps ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz \ - --snps ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps \ - --prefix ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed \ - --autoClip ${studyMerlinChrDir}/autoChunk-chr${chr}.dat \ - 2>&1 | tee ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed-minimac.log - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.dose ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.dose - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.erate ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.erate - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.info ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.info.draft ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info.draft - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed.rec ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.rec - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.imputed-minimac.log ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log - - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.dose - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.erate - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.info.draft - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed.rec - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/phaseChunk.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/phaseChunk.ftl deleted file mode 100644 index cb54764bcf..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/phaseChunk.ftl +++ /dev/null @@ -1,56 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr,chunk - -getFile ${machBin} - -getFile ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat -getFile ${studyMerlinChrPed} - -inputs "${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat" -inputs "${studyMerlinChrPed}" - -alloutputsexist \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate" \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz" \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec" \ - "${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log" - - -mkdir -p ${studyChunkChrDir} - -${machBin} \ - -d ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat \ - -p ${studyMerlinChrPed} \ - --prefix ${studyChunkChrDir}/~chunk${chunk}-chr${chr} \ - --rounds ${phasingRounds} \ - --states ${phasingStates} \ - --phase \ - 2>&1 | tee -a ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.erate ${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.gz ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}.rec ${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec - mv ${studyChunkChrDir}/~chunk${chunk}-chr${chr}-mach.log ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/preparePedMapForImputationTool.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/preparePedMapForImputationTool.ftl deleted file mode 100644 index 9d5151c04e..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/preparePedMapForImputationTool.ftl +++ /dev/null @@ -1,23 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${studyInputPedMapChr}.map -getFile ${studyInputPedMapChr}.ped - -inputs "${studyInputPedMapChr}.map" -inputs "${studyInputPedMapChr}.ped" -alloutputsexist \ - "${studyPedMapChr}.map" \ - "${studyPedMapChr}.ped" - -mkdir -p ${studyPedMapChrDir} - -#Convert SNPids to chr_pos -awk '{$2=$1"_"$4; print $0}' ${studyInputPedMapChr}.map > ${studyPedMapChr}.map - -#Copy ped file -cp ${studyInputPedMapChr}.ped ${studyPedMapChr}.ped - -putFile ${studyPedMapChr}.map -putFile ${studyPedMapChr}.ped diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/prepareStudy.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/prepareStudy.ftl deleted file mode 100644 index f67d397d27..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/prepareStudy.ftl +++ /dev/null @@ -1,77 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=8 - -#FOREACH project,chr - -getFile ${imputationToolJar} -getFile ${imputationToolJsciCoreJar} -getFile ${imputationToolGeneticaLibrariesJar} - -getFile ${studyTriTyperChrDir}/GenotypeMatrix.dat -getFile ${studyTriTyperChrDir}/Individuals.txt -getFile ${studyTriTyperChrDir}/PhenotypeInformation.txt -getFile ${studyTriTyperChrDir}/SNPMappings.txt -getFile ${studyTriTyperChrDir}/SNPs.txt -getFile ${referenceTriTyperDir}/GenotypeMatrix.dat -getFile ${referenceTriTyperDir}/Individuals.txt -getFile ${referenceTriTyperDir}/PhenotypeInformation.txt -getFile ${referenceTriTyperDir}/SNPMappings.txt -getFile ${referenceTriTyperDir}/SNPs.txt - -#inputs "${studyTriTyperChrDir}/GenotypeMatrix.dat" -#inputs "${studyTriTyperChrDir}/Individuals.txt" -#inputs "${studyTriTyperChrDir}/PhenotypeInformation.txt" -#inputs "${studyTriTyperChrDir}/SNPMappings.txt" -#inputs "${studyTriTyperChrDir}/SNPs.txt" -inputs "${referenceTriTyperDir}/GenotypeMatrix.dat" -inputs "${referenceTriTyperDir}/Individuals.txt" -inputs "${referenceTriTyperDir}/PhenotypeInformation.txt" -inputs "${referenceTriTyperDir}/SNPMappings.txt" -inputs "${referenceTriTyperDir}/SNPs.txt" -alloutputsexist "${preparedStudyDir}/chr${chr}.dat" \ -"${preparedStudyDir}/chr${chr}.map" \ -"${preparedStudyDir}/chr${chr}.markersbeagleformat" \ -"${preparedStudyDir}/chr${chr}.ped" \ -"${preparedStudyDir}/exportlog.txt" - -#If preparedStudyDir already exists delete it -if [ -d ${preparedStudyDir} ] -then - rm -r ${preparedStudyDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${preparedStudyTempDir} - - -java -Xmx8g -jar ${imputationToolJar} \ ---mode ttpmh \ ---in ${studyTriTyperChrDir} \ ---hap ${referenceTriTyperDir} \ ---out ${preparedStudyTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${preparedStudyTempDir} ${preparedStudyDir} - - putFile ${preparedStudyDir}/chr${chr}.dat - putFile ${preparedStudyDir}/chr${chr}.map - putFile ${preparedStudyDir}/chr${chr}.markersbeagleformat - putFile ${preparedStudyDir}/chr${chr}.ped - putFile ${preparedStudyDir}/exportlog.txt - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/startMinimacStage2.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/startMinimacStage2.ftl deleted file mode 100644 index c869caddb5..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/startMinimacStage2.ftl +++ /dev/null @@ -1,98 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH autostart - -getFile ${concatWorksheetsJar} - -<#list finalChunkChrWorksheet as chunkFile> - getFile ${chunkFile} - - - -inputs "${ssvQuoted(finalChunkChrWorksheet)}" -alloutputsexist \ - "${projectPhasingJobsDir}/check_for_submission.txt" \ - "${concattedChunkWorksheet}" \ - "${projectPhasingJobsDirTarGz}" - - -module load jdk/${javaversion} - -java -jar ${concatWorksheetsJar} \ - ${tmpConcattedChunkWorksheet} \ - ${ssvQuoted(finalChunkChrWorksheet)} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${tmpConcattedChunkWorksheet} ${concattedChunkWorksheet} - - putFile ${concattedChunkWorksheet} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - -#Call compute to generate phasing jobs - -mkdir -p ${projectPhasingJobsDir} - -# Execute MOLGENIS/compute to create job scripts. -sh ${McDir}/molgenis_compute.sh \ --worksheet="${concattedChunkWorksheet}" \ --parameters="${McParameters}" \ --workflow="${McProtocols}/../workflowMinimacStage2.csv" \ --protocols="${McProtocols}/" \ --templates="${McTemplates}/" \ --scripts="${projectPhasingJobsDir}/" \ --id="${McId}" - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nJob generation succesful!\n\n" - - perl -pi -e "s/sleep 8/sleep 0/" ${projectPhasingJobsDir}/submit.sh - - <#if autostart == "TRUE"> - cd ${projectPhasingJobsDir} - sh submit.sh - touch ${projectPhasingJobsDir}/check_for_submission.txt - <#elseif autostart == "FALSE"> - - echo "No autostart selected" - - echo "You can submit your jobs using the following command:" - echo "cd ${projectPhasingJobsDir}" - echo "sh submit.sh" - - - - - tar czf ${projectPhasingJobsDirTarGz} ${projectPhasingJobsDir} - putFile ${projectPhasingJobsDirTarGz} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/protocols/startMinimacStage3.ftl b/modules/compute/demo/mach_minimach/minimacStage3/protocols/startMinimacStage3.ftl deleted file mode 100644 index 84ccc247c5..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/protocols/startMinimacStage3.ftl +++ /dev/null @@ -1,73 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH autostart - -getFile ${expandWorksheetJar} - -getFile ${concattedChunkWorksheet} - -inputs "${concattedChunkWorksheet}" -alloutputsexist \ -"${projectImputationJobsDirTarGz}" \ -${projectImputationJobsDir}/check_for_submission.txt - - - - -#Call compute to generate phasing jobs -module load jdk/${javaversion} - -mkdir -p ${projectImputationJobsDir} - -# Execute MOLGENIS/compute to create job scripts. -sh ${McDir}/molgenis_compute.sh \ --worksheet="${concattedChunkWorksheet}" \ --parameters="${McParameters}" \ --workflow="${McProtocols}/../workflowMinimacStage3.csv" \ --protocols="${McProtocols}/" \ --templates="${McTemplates}/" \ --scripts="${projectImputationJobsDir}/" \ --id="${McId}" - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nJob generation succesful!\n\n" - - perl -pi -e "s/sleep 8/sleep 0/" ${projectImputationJobsDir}/submit.sh - - <#if autostart == "TRUE"> - cd ${projectImputationJobsDir} - sh submit.sh - - touch ${projectImputationJobsDir}/check_for_submission.txt - - <#elseif autostart == "FALSE"> - - echo "No autostart selected" - - echo "You can submit your jobs using the following command:" - echo "cd ${projectImputationJobsDir}" - echo "sh submit.sh" - - - - - - tar czf ${projectImputationJobsDirTarGz} ${projectImputationJobsDir} - putFile ${projectImputationJobsDirTarGz} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - diff --git a/modules/compute/demo/mach_minimach/minimacStage3/workflowMinimacStage2.csv b/modules/compute/demo/mach_minimach/minimacStage3/workflowMinimacStage2.csv deleted file mode 100644 index 34d168fcf9..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/workflowMinimacStage2.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -prePhasingMachStage2_s00,phaseChunk, -prePhasingMachStage2_s01,startMinimacStage3,prePhasingMachStage2_s00 diff --git a/modules/compute/demo/mach_minimach/minimacStage3/workflowMinimacStage3.csv b/modules/compute/demo/mach_minimach/minimacStage3/workflowMinimacStage3.csv deleted file mode 100644 index 16f01679a7..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/workflowMinimacStage3.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -imputationMinimac_s00,minimacImputation, -imputationMinimac_s01,mergeMinimacImputationResults,imputationMinimac_s00 diff --git a/modules/compute/demo/mach_minimach/minimacStage3/worksheet.csv b/modules/compute/demo/mach_minimach/minimacStage3/worksheet.csv deleted file mode 100644 index cad763688f..0000000000 --- a/modules/compute/demo/mach_minimach/minimacStage3/worksheet.csv +++ /dev/null @@ -1,7 +0,0 @@ -project,studyInputDir,referencePanel,imputationResultDir,imputationPipeline,genomeBuild,chr,chunk -gonl_release3_1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/goldStandard/celiacNlSelectedSnps/pedmap/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/celiacGoldStandardNl_Minimac_refGoNL3.1/,minimach,b37,20,1 -gonl_release3_1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/goldStandard/celiacNlSelectedSnps/pedmap/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/celiacGoldStandardNl_Minimac_refGoNL3.1/,minimach,b37,20,2 -gonl_release3_1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/goldStandard/celiacNlSelectedSnps/pedmap/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/celiacGoldStandardNl_Minimac_refGoNL3.1/,minimach,b37,20,3 -gonl_release3_1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/goldStandard/celiacNlSelectedSnps/pedmap/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/celiacGoldStandardNl_Minimac_refGoNL3.1/,minimach,b37,20,4 -gonl_release3_1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/goldStandard/celiacNlSelectedSnps/pedmap/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/celiacGoldStandardNl_Minimac_refGoNL3.1/,minimach,b37,20,5 -gonl_release3_1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/goldStandard/celiacNlSelectedSnps/pedmap/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/celiacGoldStandardNl_Minimac_refGoNL3.1/,minimach,b37,20,6 diff --git a/modules/compute/demo/mach_minimach/versionOct11/parameters.csv b/modules/compute/demo/mach_minimach/versionOct11/parameters.csv deleted file mode 100644 index d6e5d918a2..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/parameters.csv +++ /dev/null @@ -1,103 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,default,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc/,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -resdir,${root}/resources,,, -#,,,, -tempdir,${imputationResultDir}/tmp/,,, -plink,${tooldir}/plink-${plinkversion}/plink,,, -plinkversion,1.07-x86_64,,, -plinkseqBin,${tooldir}/plink-${plinkseqversion}/plink108,,, -plinkseqversion,1.08,,, -projectComputeDir,${imputationResultDir}/compute,,, -projectJobsDir,${projectComputeDir}/jobs,,, -projectChrJobsDir,${projectJobsDir}/chr${chr}/,,, -projectChrPhasingJobsDir,${projectChrJobsDir}/phasing/,,, -projectChrImputationJobsDir,${projectChrJobsDir}/imputation/,,, -projectChrPhasingJobsDirTarGz,${projectChrJobsDir}/phasing.tar.gz,,, -projectChrImputationJobsDirTarGz,${projectChrJobsDir}/imputation.tar.gz,,, -projectPhasingJobsDir,${projectJobsDir}/phasing/,,, -projectImputationJobsDir,${projectJobsDir}/imputation/,,, -projectPhasingJobsDirTarGz,${projectJobsDir}/phasing.tar.gz,,, -projectImputationJobsDirTarGz,${projectJobsDir}/imputation.tar.gz,,, -projectTempDir,${tempdir}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyInputPedMapChr,${studyInputDir}/chr${chr},,, -studyPedMapChrDir,${studyPedMapDir}/chr${chr}/,,, -studyPedMapChr,${studyPedMapChrDir}/chr${chr},,, -studyTriTyperChrTempDir,${projectTempDir}/StudyTriTyper/~chr${chr}/,end with slash,, -studyTriTyperChrDir,${projectTempDir}/StudyTriTyper/chr${chr}/,end with slash,, -preparedStudyTempDir,${projectTempDir}/preparedStudy/~${chr}/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/${chr}/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,gtool,,, -#gtoolBin,${tooldir}/gtool_${gtoolBinversion}/gtool,,, -gtoolBinversion,v0.7.5_x86_64,,, -referenceFolder,${resdir}/imputationReference/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/Chr${chr}/,end with slash,, -pythonversion,2.7.3,,, -javaversion,1.6.0_33,,, -imputationToolJar,${tooldir}/ImputationTool-${imputationToolJarversion}/ImputationTool.jar,,, -imputationToolJarversion,20120912,,, -imputationToolLibDir,${tooldir}/ImputationTool-${imputationToolJarversion}/lib/,,, -imputationToolGeneticaLibrariesJar,${imputationToolLibDir}/GeneticaLibraries.jar,,, -imputationToolJsciCoreJar,${imputationToolLibDir}/jsci-core-1.1.jar,,, -convertB36ChrTempDir,${projectTempDir}/b36conversion/,,, -convertB36ChrHg19Bed,${convertB36ChrTempDir}/chr_${chr}Hg19.bed,,, -convertB36unmapped,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -convertB36unmappedSNPs,${projectTempDir}/b36conversion/chr_${chr}.unmapped.txt,,, -b36conversionPedMapResultDir,${imputationResultDir}/b36PedMap/,,, -liftOverUcscBin,${tooldir}/liftOverUcsc-${liftOverUcscBinversion}/liftOver,,, -liftOverUcscBinversion,20120905,,, -convertB36ChrHg18Bed,${convertB36ChrTempDir}/chr_${chr}Hg18.bed,,, -liftoverDir,${resdir}/liftover/,,, -hg19ToHg18chainfile,${liftoverDir}/hg19ToHg18.over.chain,,, -project,,,,"imputationResultDir,studyInputDir,referencePanel,imputationPipeline" -expandWorksheetJar,${tooldir}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}/ExpandWorksheetWithMergeWorksheet${expandWorksheetJarversion}.jar,,, -expandWorksheetJarversion,V1.1,,, -concatWorksheetsJar,${tooldir}/ConcatWorksheets${concatWorksheetsJarversion}/ConcatWorksheets${concatWorksheetsJarversion}.jar -concatWorksheetsJarversion,V1.0,,, -#,,,, -chr,,,, -chunkSize,2500,,, -chunkOverlap,500,,, -chunkChromosomeBin,${tooldir}/ChunkChromosome-${chunkChromosomeBinVersion}/ChunkChromosome,,, -chunkChromosomeBinVersion,2012-08-28,,, -chunk,,,, -chunkChrWorkSheet,${tempdir}/tmpChr${chr}ChunkWorksheet.csv,,, -finalChunkChrWorksheet,${tempdir}/ChunkChr${chr}Worksheet.csv,,, -tmpFinalChunkChrWorksheet,${tempdir}/~ChunkChr${chr}Worksheet.csv,,, -concattedChunkWorksheet,${imputationResultDir}/concattedChunkWorksheet.csv,,, -tmpConcattedChunkWorksheet,${imputationResultDir}/~concattedChunkWorksheet.csv,,, -studyMerlinDir,${tempdir}/studyMerlin/,,, -studyMerlinChrDir,${studyMerlinDir}/chr${chr}/,,, -studyMerlinChrMap,${studyMerlinChrDir}/chr${chr}.map,,, -studyMerlinChrDat,${studyMerlinChrDir}/chr${chr}.dat,,, -studyMerlinChrPed,${studyMerlinChrDir}/chr${chr}.ped,,, -machBin,${tooldir}/mach.${machBinversion}/executables/mach1,,, -machBinversion,1.0.18,,, -studyChunkDir,${tempdir}/studyChunks,,, -studyChunkChrDir,${studyChunkDir}/chr${chr}/,,, -phasingRounds,20,,, -phasingStates,200,,, -phasingHaplotypeSampling,5,,, -minimacOmpBin,${tooldir}/minimac-beta-${minimacVersion}/minimac-omp,,, -minimacVersion,2012.10.3,,, -referenceChrVcf,${referenceFolder}/${referencePanel}/vcf/chr${chr}.vcf,,, -referenceChrVcfGz,${referenceFolder}/${referencePanel}/vcf/chr${chr}.vcf.gz,,, -#,,,, -studyInputDir,,,, -referencePanel,,,, -imputationResultDir,,,, -imputationPipeline,,,, -genomeBuild,,,, -autostart,,,, diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index 15513f7867..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 0 - diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/Footer.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/Header.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/Header.ftl deleted file mode 100644 index 32e91a79b6..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/Header.ftl +++ /dev/null @@ -1,34 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#!/bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - -<#elseif scheduler == "GRID"> - - - - -<#if scheduler != "GRID"> -# Configures the GCC bash environment -. ${root}/gcc.bashrc - - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/Helpers.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/Macros.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/NGSHeader.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/chunkChromosome.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/chunkChromosome.ftl deleted file mode 100644 index 717294b45f..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/chunkChromosome.ftl +++ /dev/null @@ -1,82 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${chunkChromosomeBin} -getFile ${expandWorksheetJar} - -getFile ${studyMerlinChrDat} -getFile ${McWorksheet} - -inputs "${studyMerlinChrDat}" -inputs "${McWorksheet}" -alloutputsexist \ - "${studyMerlinChrDir}/chunk$c-chr${chr}.dat.snps" \ - "${studyMerlinChrDir}/chunk$c-chr${chr}.dat" - -#Chunk chromosomes into pieces containing ~2500 markers - -cd ${studyMerlinChrDir} - -${chunkChromosomeBin} \ - -d ${studyMerlinChrDat} \ - -n ${chunkSize} \ - -o ${chunkOverlap} - -returnCode=$? - -if [ $returnCode -ne 0 ] -then - - echo -e "\nNon zero return code. Something went wrong creating the chunks\n\n" - #Return non zero return code - exit 1 - -fi - -#Create .csv file to be merged with original worksheet -echo "chunk" > ${chunkChrWorkSheet} - - -chunks=(${studyMerlinChrDir}/chunk*-chr${chr}.dat.snps) - -s=${r"${#chunks[*]}"} - -for c in `seq 1 $s` -do - echo $c >> ${chunkChrWorkSheet} - putFile ${studyMerlinChrDir}/chunk$c-chr${chr}.dat.snps - putFile ${studyMerlinChrDir}/chunk$c-chr${chr}.dat -done - - -#Merge worksheets -module load jdk/${javaversion} - -#Run Jar to create full worksheet - - -java -jar ${expandWorksheetJar} ${McWorksheet} ${tmpFinalChunkChrWorksheet} ${chunkChrWorkSheet} project ${project} chr ${chr} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${tmpFinalChunkChrWorksheet} ${finalChunkChrWorksheet} - - putFile ${finalChunkChrWorksheet} - - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/convertPedMapToTriTyper.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/convertPedMapToTriTyper.ftl deleted file mode 100644 index 2226531068..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/convertPedMapToTriTyper.ftl +++ /dev/null @@ -1,61 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${imputationToolJar} -getFile ${imputationToolJsciCoreJar} -getFile ${imputationToolGeneticaLibrariesJar} - -getFile ${studyPedMapChr}.map -getFile ${studyPedMapChr}.ped - - - -inputs "${studyPedMapChr}.map" -inputs "${studyPedMapChr}.ped" -alloutputsexist "${studyTriTyperChrDir}/GenotypeMatrix.dat" \ -"${studyTriTyperChrDir}/Individuals.txt" \ -"${studyTriTyperChrDir}/PhenotypeInformation.txt" \ -"${studyTriTyperChrDir}/SNPMappings.txt" \ -"${studyTriTyperChrDir}/SNPs.txt" - - -if [ -d ${studyTriTyperChrDir} ] -then - rm -r ${studyTriTyperChrDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${studyTriTyperChrTempDir} - -java -jar ${imputationToolJar} \ ---mode pmtt \ ---in ${studyPedMapChrDir} \ ---out ${studyTriTyperChrTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${studyTriTyperChrTempDir} ${studyTriTyperChrDir} - - putFile "${studyTriTyperChrDir}/GenotypeMatrix.dat" - putFile "${studyTriTyperChrDir}/Individuals.txt" - putFile "${studyTriTyperChrDir}/PhenotypeInformation.txt" - putFile "${studyTriTyperChrDir}/SNPMappings.txt" - putFile "${studyTriTyperChrDir}/SNPs.txt" - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/convertPlinkPedMapToMerlin.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/convertPlinkPedMapToMerlin.ftl deleted file mode 100644 index 2f610b12bc..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/convertPlinkPedMapToMerlin.ftl +++ /dev/null @@ -1,36 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${studyPedMapChr}.map -getFile ${studyPedMapChr}.ped - -inputs ${studyPedMapChr}.map -inputs ${studyPedMapChr}.ped - - -alloutputsexist \ -"${studyMerlinChrMap}" \ -"${studyMerlinChrDat}" \ -"${studyMerlinChrPed}" - -mkdir -p ${studyMerlinChrDir} - -#Conver SNP ID to chr_pos and remove 3e column to adhere to merlin -gawk ' - BEGIN {$1="CHROMOSOME";$2="MARKER";$3="POSITION";print $0} - {$2=$1":"$4;print $1,$2,$4} -' OFS="\t" ${studyPedMapChr}.map > ${studyMerlinChrMap} - -gawk 'BEGIN {print "T","pheno";}{print "M",$1":"$4}' ${studyPedMapChr}.map > ${studyMerlinChrDat} - -#Copy ped file -cp ${studyPedMapChr}.ped ${studyMerlinChrPed} - - - -putFile ${studyMerlinChrMap} -putFile ${studyMerlinChrDat} -putFile ${studyMerlinChrPed} - - diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/minimacImputation.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/minimacImputation.ftl deleted file mode 100644 index ee7255fc81..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/minimacImputation.ftl +++ /dev/null @@ -1,49 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=4 mem=4 - -#FOREACH project,chr,chunk - -getFile ${minimacOmpBin} - -getFile ${referenceChrVcfGz} -getFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz -getFile ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps - -inputs "${referenceChrVcfGz}" \ -inputs "${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz" \ -inputs "${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps" - -${minimacOmpBin} \ ---cpus 4 \ ---refHaps ${referenceChrVcfGz} \ ---vcfReference \ ---haps ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz \ ---snps ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat.snps \ ---prefix ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed \ ->& ${studyChunkChrDir}/chunk${chunk}-chr${chr}.imputed-minimac.log & - -######################################### -##############FIX THIS LATER############# -######################################### - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - #mv ${tmpFinalChunkChrWorksheet} ${finalChunkChrWorksheet} - - #putFile ${finalChunkChrWorksheet} - - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/phaseChunk.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/phaseChunk.ftl deleted file mode 100644 index 462193d6ec..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/phaseChunk.ftl +++ /dev/null @@ -1,50 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr,chunk - -getFile ${machBin} - -getFile ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat -getFile ${studyMerlinChrPed} - -inputs "${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat" -inputs "${studyMerlinChrPed}" -alloutputsexist \ -"${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate" \ -"${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz" \ -"${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec" \ -"${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log" - - -mkdir -p ${studyChunkChrDir} - -${machBin} \ --d ${studyMerlinChrDir}/chunk${chunk}-chr${chr}.dat \ --p ${studyMerlinChrPed} \ ---prefix ${studyChunkChrDir}/chunk${chunk}-chr${chr} \ ---rounds ${phasingRounds} \ ---states ${phasingStates} \ ---phase \ -2>&1 | tee -a ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - -###REMOVED --sample ${phasingHaplotypeSampling} from command -###If used files with extension *.sample1, *.sample6, *.sample11, *.sample16 etc are created - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.erate - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.gz - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}.rec - putFile ${studyChunkChrDir}/chunk${chunk}-chr${chr}-mach.log - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/preparePedMapForImputationTool.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/preparePedMapForImputationTool.ftl deleted file mode 100644 index a89bd5df6d..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/preparePedMapForImputationTool.ftl +++ /dev/null @@ -1,23 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - -#FOREACH project,chr - -getFile ${studyInputPedMapChr}.map -getFile ${studyInputPedMapChr}.ped - -inputs "${studyInputPedMapChr}.map" -inputs "${studyInputPedMapChr}.ped" -alloutputsexist \ -"${studyPedMapChr}.map" \ -"${studyPedMapChr}.ped" - -mkdir -p ${studyPedMapChrDir} - -#Convert SNPids to chr_pos -awk '{$2=$1"_"$4; print $0}' ${studyInputPedMapChr}.map > ${studyPedMapChr}.map - -#Copy ped file -cp ${studyInputPedMapChr}.ped ${studyPedMapChr}.ped - -putFile ${studyPedMapChr}.map -putFile ${studyPedMapChr}.ped diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/prepareStudy.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/prepareStudy.ftl deleted file mode 100644 index f031951851..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/prepareStudy.ftl +++ /dev/null @@ -1,77 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=8 - -#FOREACH project,chr - -getFile ${imputationToolJar} -getFile ${imputationToolJsciCoreJar} -getFile ${imputationToolGeneticaLibrariesJar} - -getFile ${studyTriTyperChrDir}/GenotypeMatrix.dat -getFile ${studyTriTyperChrDir}/Individuals.txt -getFile ${studyTriTyperChrDir}/PhenotypeInformation.txt -getFile ${studyTriTyperChrDir}/SNPMappings.txt -getFile ${studyTriTyperChrDir}/SNPs.txt -getFile ${referenceTriTyperDir}/GenotypeMatrix.dat -getFile ${referenceTriTyperDir}/Individuals.txt -getFile ${referenceTriTyperDir}/PhenotypeInformation.txt -getFile ${referenceTriTyperDir}/SNPMappings.txt -getFile ${referenceTriTyperDir}/SNPs.txt - -inputs "${studyTriTyperChrDir}/GenotypeMatrix.dat" -inputs "${studyTriTyperChrDir}/Individuals.txt" -inputs "${studyTriTyperChrDir}/PhenotypeInformation.txt" -inputs "${studyTriTyperChrDir}/SNPMappings.txt" -inputs "${studyTriTyperChrDir}/SNPs.txt" -inputs "${referenceTriTyperDir}/GenotypeMatrix.dat" -inputs "${referenceTriTyperDir}/Individuals.txt" -inputs "${referenceTriTyperDir}/PhenotypeInformation.txt" -inputs "${referenceTriTyperDir}/SNPMappings.txt" -inputs "${referenceTriTyperDir}/SNPs.txt" -alloutputsexist "${preparedStudyDir}/chr${chr}.dat" \ -"${preparedStudyDir}/chr${chr}.map" \ -"${preparedStudyDir}/chr${chr}.markersbeagleformat" \ -"${preparedStudyDir}/chr${chr}.ped" \ -"${preparedStudyDir}/exportlog.txt" - -#If preparedStudyDir already exists delete it -if [ -d ${preparedStudyDir} ] -then - rm -r ${preparedStudyDir} -fi - - -module load jdk/${javaversion} - -mkdir -p ${preparedStudyTempDir} - - -java -Xmx8g -jar ${imputationToolJar} \ ---mode ttpmh \ ---in ${studyTriTyperChrDir} \ ---hap ${referenceTriTyperDir} \ ---out ${preparedStudyTempDir} - - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${preparedStudyTempDir} ${preparedStudyDir} - - putFile ${preparedStudyDir}/chr${chr}.dat - putFile ${preparedStudyDir}/chr${chr}.map - putFile ${preparedStudyDir}/chr${chr}.markersbeagleformat - putFile ${preparedStudyDir}/chr${chr}.ped - putFile ${preparedStudyDir}/exportlog.txt - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/startMinimacStage2.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/startMinimacStage2.ftl deleted file mode 100644 index e719d43c74..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/startMinimacStage2.ftl +++ /dev/null @@ -1,98 +0,0 @@ -#MOLGENIS walltime=05:00:00 nodes=1 cores=1 mem=4 - - -getFile ${concatWorksheetsJar} - -<#list finalChunkChrWorkSheet as chunkFile> - getFile ${chunkFile} - - - -inputs "${ssvQuoted(finalChunkChrWorkSheet)}" -alloutputsexist \ - "${projectPhasingJobsDir}/check_for_submission.txt" \ - "${concattedChunkWorksheet}" \ - "${projectPhasingJobsDirTarGz}" - - -module load jdk/${javaversion} - -java -jar ${concatWorksheetsJar} \ - ${tmpConcattedChunkWorksheet} \ - ${ssvQuoted(finalChunkChrWorkSheet)} - -#Get return code from last program call -returnCode=$? - -if [ $returnCode -eq 0 ] -then - - echo -e "\nMoving temp files to final files\n\n" - - mv ${tmpConcattedChunkWorksheet} ${concattedChunkWorksheet} - - putFile ${concattedChunkWorksheet} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - - - -#Call compute to generate phasing jobs - -mkdir -p ${projectPhasingJobsDir} - -# Execute MOLGENIS/compute to create job scripts. -sh ${McDir}/molgenis_compute.sh \ --worksheet=${concattedChunkWorksheet} \ --parameters=${McParameters} \ --workflow=${McProtocols}/../workflowMinimacStage2.csv \ --protocols=${McProtocols}/ \ --templates=${McTemplates}/ \ --scripts=${projectPhasingJobsDir}/ \ --id=${McId} - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nJob generation succesful!\n\n" - - <#if autostart == "TRUE"> - cd ${projectPhasingJobsDir} - sh submit.sh - touch ${projectPhasingJobsDir}/check_for_submission.txt - <#elseif autostart == "FALSE"> - - echo "No autostart selected" - - echo "You can submit your jobs using the following command:" - echo "cd ${projectPhasingJobsDir}" - echo "sh submit.sh" - - - - - tar czf ${projectPhasingJobsDirTarGz} ${projectPhasingJobsDir} - putFile ${projectPhasingJobsDirTarGz} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - - diff --git a/modules/compute/demo/mach_minimach/versionOct11/protocols/startMinimacStage3.ftl b/modules/compute/demo/mach_minimach/versionOct11/protocols/startMinimacStage3.ftl deleted file mode 100644 index 7a55dc07d7..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/protocols/startMinimacStage3.ftl +++ /dev/null @@ -1,71 +0,0 @@ -#MOLGENIS walltime=96:00:00 nodes=1 cores=1 mem=4 - - - -getFile ${expandWorksheetJar} - -getFile ${concattedChunkWorksheet} - -inputs "${concattedChunkWorksheet}" -alloutputsexist \ -"${projectImputationJobsDirTarGz}" \ -${projectImputationJobsDir}/check_for_submission.txt - - - - -#Call compute to generate phasing jobs -module load jdk/${javaversion} - -mkdir -p ${projectImputationJobsDir} - -# Execute MOLGENIS/compute to create job scripts. -sh ${McDir}/molgenis_compute.sh \ --worksheet=${concattedChunkWorksheet} \ --parameters=${McParameters} \ --workflow=${McProtocols}/../workflowMinimacStage3.csv \ --protocols=${McProtocols}/ \ --templates=${McTemplates}/ \ --scripts=${projectImputationJobsDir}/ \ --id=${McId} - - -#Get return code from last program call -returnCode=$? - - -if [ $returnCode -eq 0 ] -then - - echo -e "\nJob generation succesful!\n\n" - - <#if autostart == "TRUE"> - cd ${projectImputationJobsDir} - sh submit.sh - - touch ${projectImputationJobsDir}/check_for_submission.txt - - <#elseif autostart == "FALSE"> - - echo "No autostart selected" - - echo "You can submit your jobs using the following command:" - echo "cd ${projectImputationJobsDir}" - echo "sh submit.sh" - - - - - - tar czf ${projectImputationJobsDirTarGz} ${projectImputationJobsDir} - putFile ${projectImputationJobsDirTarGz} - -else - - echo -e "\nNon zero return code not making files final. Existing temp files are kept for debuging purposes\n\n" - #Return non zero return code - exit 1 - -fi - - diff --git a/modules/compute/demo/mach_minimach/versionOct11/workflowMinimacStage1.csv b/modules/compute/demo/mach_minimach/versionOct11/workflowMinimacStage1.csv deleted file mode 100644 index 44bf4c0eb3..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/workflowMinimacStage1.csv +++ /dev/null @@ -1,7 +0,0 @@ -name,protocol_name,PreviousSteps_name -prePhasingMach_s00,preparePedMapForImputationTool, -prePhasingMach_s01,convertPedMapToTriTyper,preparePedMapForImputationTool -prePhasingMach_s02,prepareStudy,convertPedMapToTriTyper -prePhasingMach_s03,convertPlinkPedMapToMerlin,prepareStudy -prePhasingMach_s04,chunkChromosome,convertPlinkPedMapToMerlin -prePhasingMach_s05,startMinimacStage2,chunkChromosome diff --git a/modules/compute/demo/mach_minimach/versionOct11/worksheet.csv b/modules/compute/demo/mach_minimach/versionOct11/worksheet.csv deleted file mode 100755 index caf8a5b6c3..0000000000 --- a/modules/compute/demo/mach_minimach/versionOct11/worksheet.csv +++ /dev/null @@ -1,28 +0,0 @@ -project,studyInputDir,referencePanel,imputationResultDir,imputationPipeline,genomeBuild -1240Blood_b37,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Impute2_refGoNL_allChrs,impute2,b37 - - - -project,studyInputDir,referencePanel,imputationResultDir,imputationPipeline,genomeBuild,chr,autostart -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,1,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,2,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,3,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,4,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,5,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,6,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,7,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,8,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,9,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,10,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,11,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,12,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,13,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,14,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,15,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,16,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,17,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,18,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,19,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,20,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,21,TRUE -gonl_release3.1,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/1240Blood/MapPedB37/,gonl_release3.1,/target/gpfs2/gcc/groups/gonl/projects/imputationBenchmarking/imputationResult/1240Blood_Minimac_refGoNL_allChrs/,minimach,b37,22,TRUE diff --git a/modules/compute/demo/mach_minimach/versionSept14/parameters.csv b/modules/compute/demo/mach_minimach/versionSept14/parameters.csv deleted file mode 100644 index d4a9639f43..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept14/parameters.csv +++ /dev/null @@ -1,53 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -workflowFile,${McDir}/protocols/imputation/workflowBeagle.csv,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -plink,${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -homedir,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/,,, -projectdir,${homedir}/${project},,, -projectTempDir,${tempdir}/${McId}/${project}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyTriTyperTempDir,${projectTempDir}/~StudyTriTyper/,end with slash,, -studyTriTyperDir,${projectTempDir}/StudyTriTyper/,end with slash,, -preparedStudyTempDir,${projectTempDir}/~preparedStudy/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,${tooldir}/gtool_v0.7.5_x86_64>/gtool,,, -referenceFolder,${resdir}/imputation/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/,end with slash,, -referenceImpute2Dir,${referenceFolder}/${referencePanel}/Impute2/,end with slash,, -impute2Bin,${tooldir}/impute_v2.2.2_x86_64_static/impute2,,, -imputationToolJar,${tooldir}/ImputationTool/dist/ImputationTool2.jar,,, -referenceImpute2HapFile,${referenceImpute2Dir}/${chr}.hap -referenceImpute2LegendFile,${referenceImpute2Dir}/${chr}.legend -referenceImpute2MapFile,${referenceImpute2Dir}/${chr}.map -impute2ResultDir,${projectTempDir}/Impute2Result/,end with slash,, -calculateBeagleR2ForIMpute2ResultsPythonScript,${tooldir}/python_scripts/calculateBeagleR2ForImpute2Results.py,,, -impute2ResultChrBinTemp,${impute2ResultDir}/${chr}/~chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBin,${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBinGenFile,${impute2ResultChrBin}.gen,Ask alex for correct file extension,, -impute2ResultChrBinInfoFile,${impute2ResultChrBin}.info,,, -project,,,,"imputationResult,studyInputPedMap,referencePanel" diff --git a/modules/compute/demo/mach_minimach/versionSept14/protocols/preparePedMapForImpute2.ftl b/modules/compute/demo/mach_minimach/versionSept14/protocols/preparePedMapForImpute2.ftl deleted file mode 100644 index edf8d1be49..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept14/protocols/preparePedMapForImpute2.ftl +++ /dev/null @@ -1,9 +0,0 @@ - -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 -#INPUTS imputationResult/chr_${chr} -#OUTPUTS imputationResult/chr_${chr}.beagleR2 -#EXES calculateBeagleR2ForIMpute2ResultsPythonScript -#LOGS log -#TARGETS project,chr -#FOREACH project,chr - diff --git a/modules/compute/demo/mach_minimach/versionSept14/workflow.csv b/modules/compute/demo/mach_minimach/versionSept14/workflow.csv deleted file mode 100644 index 3cc118d7e6..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept14/workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -impute2_s1,preparePedMapForImpute2, diff --git a/modules/compute/demo/mach_minimach/versionSept14/worksheet.csv b/modules/compute/demo/mach_minimach/versionSept14/worksheet.csv deleted file mode 100644 index 82f1514cea..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept14/worksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,referencePanel,chr,fromChrPos,toChrPos -proj001,1000Genomes,20,5000000,10000000 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/CustomSubmit.sh.ftl b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/CustomSubmit.sh.ftl deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/Footer.ftl b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/Footer.ftl deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/Header.ftl b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/Header.ftl deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/impute_with_minimac.ftl b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/impute_with_minimac.ftl deleted file mode 100644 index 6403de8735..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/impute_with_minimac.ftl +++ /dev/null @@ -1,31 +0,0 @@ - -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 -#INPUTS ${referencePanel},${preparedStudyDir}/chr${chr}.dat,${preparedStudyDir}/chr${chr}.gz,${preparedStudyDir}/chr${chr}.snps -#OUTPUTS ${preparedStudyDir}/chr${chr}.results -#EXES ${minimacBin} -#LOGS log -#TARGETS project,referencePanel,chr - -#FOREACH project,referencePanel,chr - -inputs "${referencePanel}" -inputs "${preparedStudyDir}/chr${chr}.gz" -inputs "${preparedStudyDir}/chr${chr}.dat" -inputs "${preparedStudyDir}/chr${chr}.snps" -alloutputsexist "${preparedStudyDir}/chr${chr}.results" - -#Minimac requires a file listing markers in the haplotype file. This file can be easily -#generated by extracting the second column from the .dat file. - -cut -f 2 -d " " ${preparedStudyDir}/chr${chr}.dat > ${preparedStudyDir}/chr${chr}.snps - -#Example -#cut -f 2 -d " " examples/sample.dat > examples/sample.snps - -#The imputation step -${minimacBin} --vcfReference --refHaps ${referencePanel} --haps ${preparedStudyDir}/chr${chr}.gz --snps ${preparedStudyDir}/chr${chr}.snps --rounds 5 --states 200 --prefix ${preparedStudyDir}/chr${chr}.results - - -#Example: -#./minimac --vcfReference --refHaps /target/gpfs2/gcc/resources/ImputationReferenceSets/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL/chr10.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --haps mach1.out.gz --snps examples/sample.snps --rounds 5 --states 200 --prefix results - diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/parameters.csv b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/parameters.csv deleted file mode 100644 index 0bbe9439f0..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/parameters.csv +++ /dev/null @@ -1,55 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -workflowFile,${McDir}/protocols/imputation/workflowBeagle.csv,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -plink,${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -#homedir,${root}/home/fvandijk,,, -homedir,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/,,, -projectdir,${homedir}/${project},,, -projectTempDir,${tempdir}/${McId}/${project}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyTriTyperTempDir,${projectTempDir}/~StudyTriTyper/,end with slash,, -studyTriTyperDir,${projectTempDir}/StudyTriTyper/,end with slash,, -preparedStudyTempDir,${projectTempDir}/~preparedStudy/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,${tooldir}/gtool_v0.7.5_x86_64>/gtool,,, -machBin,${tooldir}/mach/executables/mach1,,, -minimacBin,${tooldir}/minimac-beta-2012.8.15/minimac,,, -referenceFolder,${resdir}/imputation/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/,end with slash,, -referenceImpute2Dir,${referenceFolder}/${referencePanel}/Impute2/,end with slash,, -impute2Bin,${tooldir}/impute_v2.2.2_x86_64_static/impute2,,, -imputationToolJar,${tooldir}/ImputationTool/dist/ImputationTool2.jar,,, -referenceImpute2HapFile,${referenceImpute2Dir}/${chr}.hap -referenceImpute2LegendFile,${referenceImpute2Dir}/${chr}.legend -referenceImpute2MapFile,${referenceImpute2Dir}/${chr}.map -impute2ResultDir,${projectTempDir}/Impute2Result/,end with slash,, -calculateBeagleR2ForIMpute2ResultsPythonScript,${tooldir}/python_scripts/calculateBeagleR2ForImpute2Results.py,,, -impute2ResultChrBinTemp,${impute2ResultDir}/${chr}/~chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBin,${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBinGenFile,${impute2ResultChrBin}.gen,Ask alex for correct file extension,, -impute2ResultChrBinInfoFile,${impute2ResultChrBin}.info,,, diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/phase_study_with_mach.ftl b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/phase_study_with_mach.ftl deleted file mode 100644 index 1ecaf7df54..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/phase_study_with_mach.ftl +++ /dev/null @@ -1,25 +0,0 @@ - -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#INPUTS ${preparedStudyDir}/chr${chr}.ped,preparedStudyDir/chr${chr}.dat -#OUTPUTS ${preparedStudyDir}/chr${chr}.gz -#EXES ${machBin} -#LOGS log -#TARGETS project,chr - -#FOREACH project,chr - -inputs "${preparedStudyDir}/chr${chr}.ped" -inputs "${preparedStudyDir}/chr${chr}.dat" -alloutputsexist "${preparedStudyDir}/chr${chr}.gz" - - -#Use mach to phase the study panel. The command should be like -${machBin} -d ${preparedStudyDir}/chr${chr}.dat -p ${preparedStudyDir}/chr${chr}.ped --rounds 20 --states 20 --phase --interim 5 --compact --prefix ${preparedStudyDir}/~chr${chr} - -#Example -# ./executables/mach1 -d examples/sample.dat -p examples/sample.ped --rounds 20 --states 20 --phase --interim 5 --compact - -#Remove intermediate preliminary data if the previous step was correct -rm ${preparedStudyDir}/~chr${chr}.prelim* - diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/parameters.csv b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/parameters.csv deleted file mode 100644 index 0bbe9439f0..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/parameters.csv +++ /dev/null @@ -1,55 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,PBS,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -workflowFile,${McDir}/protocols/imputation/workflowBeagle.csv,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -plink,${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -#homedir,${root}/home/fvandijk,,, -homedir,${root}/groups/gonl/projects/imputationBenchmarking/eQtl/,,, -projectdir,${homedir}/${project},,, -projectTempDir,${tempdir}/${McId}/${project}/,end with slash,, -studyPedMapDir,${projectTempDir}/PedMap/,end with slash,, -studyTriTyperTempDir,${projectTempDir}/~StudyTriTyper/,end with slash,, -studyTriTyperDir,${projectTempDir}/StudyTriTyper/,end with slash,, -preparedStudyTempDir,${projectTempDir}/~preparedStudy/,end with slash,, -preparedStudyDir,${projectTempDir}/preparedStudy/,end with slash,, -studyPedMap,${studyPedMapDir}/,,, -gtoolBin,${tooldir}/gtool_v0.7.5_x86_64>/gtool,,, -machBin,${tooldir}/mach/executables/mach1,,, -minimacBin,${tooldir}/minimac-beta-2012.8.15/minimac,,, -referenceFolder,${resdir}/imputation/,Maybe change this path later,, -referenceTriTyperDir,${referenceFolder}/${referencePanel}/TriTyper/,end with slash,, -referenceImpute2Dir,${referenceFolder}/${referencePanel}/Impute2/,end with slash,, -impute2Bin,${tooldir}/impute_v2.2.2_x86_64_static/impute2,,, -imputationToolJar,${tooldir}/ImputationTool/dist/ImputationTool2.jar,,, -referenceImpute2HapFile,${referenceImpute2Dir}/${chr}.hap -referenceImpute2LegendFile,${referenceImpute2Dir}/${chr}.legend -referenceImpute2MapFile,${referenceImpute2Dir}/${chr}.map -impute2ResultDir,${projectTempDir}/Impute2Result/,end with slash,, -calculateBeagleR2ForIMpute2ResultsPythonScript,${tooldir}/python_scripts/calculateBeagleR2ForImpute2Results.py,,, -impute2ResultChrBinTemp,${impute2ResultDir}/${chr}/~chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBin,${impute2ResultDir}/${chr}/chr_${chr}_from_${fromChrPos}_to_${toChrPos},,, -impute2ResultChrBinGenFile,${impute2ResultChrBin}.gen,Ask alex for correct file extension,, -impute2ResultChrBinInfoFile,${impute2ResultChrBin}.info,,, diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/runlocal.sh b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/runlocal.sh deleted file mode 100644 index d747bda134..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/runlocal.sh +++ /dev/null @@ -1,11 +0,0 @@ -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/workflow_csv.started -export PBS_O_WORKDIR=${DIR} -echo Starting with s00_impute2_s1_1... -sh s00_impute2_s1_1.sh -#Dependencies: - -echo Starting with s01_impute2_s2_1... -sh s01_impute2_s2_1.sh -#Dependencies: -W depend=afterok:$s00_impute2_s1_proj001_20 - diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/s00_impute2_s1_1.sh b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/s00_impute2_s1_1.sh deleted file mode 100644 index 80f8d4756e..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/s00_impute2_s1_1.sh +++ /dev/null @@ -1,26 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 - -#INPUTS /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.ped,preparedStudyDir/chr20.dat -#OUTPUTS /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.gz -#EXES /target/gpfs2/gcc/tools/mach/executables/mach1 -#LOGS log -#TARGETS project,chr - -#FOREACH project,chr - -inputs "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.ped" -inputs "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.dat" -alloutputsexist "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.gz" - - -#Use mach to phase the study panel. The command should be like -/target/gpfs2/gcc/tools/mach/executables/mach1 -d /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.dat -p /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.ped --rounds 20 --states 20 --phase --interim 5 --compact --prefix /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//~chr20 - -#Example -# ./executables/mach1 -d examples/sample.dat -p examples/sample.ped --rounds 20 --states 20 --phase --interim 5 --compact - -#Remove intermediate preliminary data if the previous step was correct -rm /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//~chr20.prelim* - - - diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/s01_impute2_s2_1.sh b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/s01_impute2_s2_1.sh deleted file mode 100644 index f83315edba..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/s01_impute2_s2_1.sh +++ /dev/null @@ -1,32 +0,0 @@ -#MOLGENIS walltime=48:00:00 nodes=1 cores=1 mem=4 -#INPUTS aaa,/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.dat,/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.gz,/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.snps -#OUTPUTS /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.results -#EXES /target/gpfs2/gcc/tools/minimac-beta-2012.8.15/minimac -#LOGS log -#TARGETS project,referencePanel,chr - -#FOREACH project,referencePanel,chr - -inputs "aaa" -inputs "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.gz" -inputs "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.dat" -inputs "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.snps" -alloutputsexist "/target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.results" - -#Minimac requires a file listing markers in the haplotype file. This file can be easily -#generated by extracting the second column from the .dat file. - -cut -f 2 -d " " /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.dat > /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.snps - -#Example -#cut -f 2 -d " " examples/sample.dat > examples/sample.snps - -#The imputation step -/target/gpfs2/gcc/tools/minimac-beta-2012.8.15/minimac --vcfReference --refHaps aaa --haps /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.gz --snps /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.snps --rounds 5 --states 200 --prefix /target/gpfs2/gcc/tmp/processing/demo/proj001//preparedStudy//chr20.results - - -#Example: -#./minimac --vcfReference --refHaps /target/gpfs2/gcc/resources/ImputationReferenceSets/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL/chr10.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz --haps mach1.out.gz --snps examples/sample.snps --rounds 5 --states 200 --prefix results - - - diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/submit.sh b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/submit.sh deleted file mode 100644 index d5499efee2..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/submit.sh +++ /dev/null @@ -1,10 +0,0 @@ -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/workflow_csv.started -#s00_impute2_s1_1 -s00_impute2_s1_1=$(qsub -N s00_impute2_s1_1 s00_impute2_s1_1.sh) -echo $s00_impute2_s1_1 -sleep 8 -#s01_impute2_s2_1 -s01_impute2_s2_1=$(qsub -N s01_impute2_s2_1 -W depend=afterok:$s00_impute2_s1_proj001_20 s01_impute2_s2_1.sh) -echo $s01_impute2_s2_1 -sleep 8 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/submitCustom.sh b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/submitCustom.sh deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/workflow.csv b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/workflow.csv deleted file mode 100644 index 01b8b5cf38..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/workflow.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -impute2_s1,phase_study_with_mach, -impute2_s2,impute_with_minimac,impute2_s1 \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/worksheet.csv b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/worksheet.csv deleted file mode 100644 index 4e37289a19..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/scripts/worksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,referencePanel,chr,fromChrPos,toChrPos -proj001,aaa,20,5000000,10000000 diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/workflow.csv b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/workflow.csv deleted file mode 100644 index 01b8b5cf38..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/workflow.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -impute2_s1,phase_study_with_mach, -impute2_s2,impute_with_minimac,impute2_s1 \ No newline at end of file diff --git a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/worksheet.csv b/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/worksheet.csv deleted file mode 100644 index 4e37289a19..0000000000 --- a/modules/compute/demo/mach_minimach/versionSept18/mach_minimach/worksheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,referencePanel,chr,fromChrPos,toChrPos -proj001,aaa,20,5000000,10000000 diff --git a/modules/compute/demo/run0482/compute2/generate.sh b/modules/compute/demo/run0482/compute2/generate.sh deleted file mode 100644 index 8b30d94216..0000000000 --- a/modules/compute/demo/run0482/compute2/generate.sh +++ /dev/null @@ -1,20 +0,0 @@ -# -# A script to make testing of MOLGENIS/COMPUTE easier -# -# ===================================================== -# $Id$ -# $URL: http://www.bbmriwiki.nl/svn/ngs_scripts/trunk/extract_samples_from_GAF_list.pl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: mdijkstra $ -# ===================================================== -# - -sh $(dirname -- "$0")/molgenis_compute-f6e477a/molgenis_compute.sh \ --worksheet=/Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/demo/run0482/run0482.csv \ --parameters=/Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/workflows/in-house_parameters_pipeline.target.rug.nl.csv \ --workflow=/Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/workflows/in-house_workflow_data_archiving.csv \ --protocols=/Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/protocols \ --scripts=$(dirname -- "$0")/generatedscripts \ --templates=/Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/protocols \ --id=run01 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/DOIT.sh b/modules/compute/demo/run0482/compute2/generatedscripts/DOIT.sh deleted file mode 100644 index 8c48170f43..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/DOIT.sh +++ /dev/null @@ -1 +0,0 @@ -sh runlocal.sh > runlocal.log 2>&1 & \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/in-house_parameters_pipeline.target.rug.nl.csv b/modules/compute/demo/run0482/compute2/generatedscripts/in-house_parameters_pipeline.target.rug.nl.csv deleted file mode 100644 index c8e0515e87..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/in-house_parameters_pipeline.target.rug.nl.csv +++ /dev/null @@ -1,85 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -defaultInterpreter,#!/bin/bash,,, -library,${fileprefix},,, -jobname,jobname,,string, -root,/scratch1,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -workflowHeader,NGSHeader.ftl,,, -tooldir,${root}/tools,root dir for tools,string, -gafhome,/scratch1,gaf home dir,string, -gaftools,${gafhome}/tools,,string, -gafscripts,${gaftools}/scripts,,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -demultiplexWorkflowFile,${McDir}/workflows/in-house_workflow_demultiplex.csv,,string, -JAVA_HOME,/target/gpfs2/gcc/tools/jdk/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -datadir,${root}/groups/in-house,root dir for data,string, -allRawNgsDataDir,${datadir}/rawdata/ngs/,"Contains all rawdata (i.e., *.fq files)",string, -allRunDemultiplexDir,${datadir}/runs/,Demultiplex historical data specific runs directory,string, -runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell},,string, -runJobsDir,${allRunDemultiplexDir}/${runPrefix}/jobs/,Run specific job scripts directory,string, -runResultsDir,${allRunDemultiplexDir}/${runPrefix}/results/,Store demultiplexed results here,string, -rawdatadir,${allRawNgsDataDir}/${runPrefix},"contains rawdata (i.e., *.fq files)",string, -arraydir,${datadir}/rawdata/array,,, -fileprefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane},first part of file name,string, -sequencingStartDate,,,, -sequencer,,,, -run,,,,"sequencer,sequencingStartDate,runJobsDir,runResultsDir" -flowcell,,,,"run,runJobsDir,runResultsDir" -seqType,,,, -lane,,,,"flowcell,seqType" -barcode,,,, -file,, -#,,,, -filenamePartSeperator,_,,, -filenamePrefix,${sequencingStartDate}${filenamePartSeperator}${sequencer}${filenamePartSeperator}${run}${filenamePartSeperator}${flowcell}${filenamePartSeperator}L${lane},,string, -fastqExtension,.fq,,string, -gzipExtension,.gz,,string, -md5sumExtension,.md5,,string, -#,,,, -filenameSuffixPE1,1,,, -filenameSuffixPE2,2,,, -filenameSuffixDiscardedReads,DISCARDED,,, -#,,,, -fastqFilenameSR,${filenamePrefix}${fastqExtension},,, -fastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -#,,,, -compressedFastqFilenameSR,${fastqFilenameSR}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE1,${fastqFilenamePE1}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE2,${fastqFilenamePE2}${gzipExtension},use these for multiplexed files,string, -#,,,, -demultiplexedSampleFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilenameSR,${demultiplexedSampleFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilepathSR,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR},,, -compressedDemultiplexedSampleFastqFilepathPE1,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1},,, -compressedDemultiplexedSampleFastqFilepathPE2,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2},,, -#,,,, -demultiplexedSampleFastqChecksumFilenameSR,${demultiplexedSampleFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -log,log.log,,, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/in-house_workflow_data_archiving.csv b/modules/compute/demo/run0482/compute2/generatedscripts/in-house_workflow_data_archiving.csv deleted file mode 100644 index c023d32f9e..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/in-house_workflow_data_archiving.csv +++ /dev/null @@ -1,5 +0,0 @@ -name,protocol_name,PreviousSteps_name -RunGerald,RunGerald, -CopyFqToRawdatadir,CopyFqToRawdatadir,RunGerald -Demultiplex,Demultiplex,CopyFqToRawdatadir -CreateFinalReport,CreateFinalReport, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/run0482.csv b/modules/compute/demo/run0482/compute2/generatedscripts/run0482.csv deleted file mode 100644 index 08beb6c36a..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/run0482.csv +++ /dev/null @@ -1,44 +0,0 @@ -0,internalSampleID,externalSampleID,project,contact,validationLog,labStatusPhase,labStatusComments,lastUpDate,sequencingStartDate,sequencer,run,flowcell,lane,barcodeMenu,seqType,prepKit,capturingKit,arrayFile,arrayID,GAF_QC_Name,GAF_QC_Date,GAF_QC_Status,GCC_Analysis,GCC_QC_Name,GCC_QC_Date,GCC_QC_Status,TargetDateShipment,DataShippedDate,DataShippedTo,DataShippedBy,Comments,barcode,barcodeType -,1208,2048,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 02 CGATGT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CGATGT,RPI -,1209,2049,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 03 TTAGGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,TTAGGC,RPI -,1210,2050,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 04 TGACCA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,TGACCA,RPI -,1211,2051,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 05 ACAGTG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACAGTG,RPI -,1212,2055,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 09 GATCAG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GATCAG,RPI -,1213,Serum_0102,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 33 CAGGCG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAGGCG,RPI -,1214,CSF_473,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 27 ATTCCT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATTCCT,RPI -,1215,H2O,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 06 GCCAAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GCCAAT,RPI -,1216,2047,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 01 ATCACG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATCACG,RPI -,1217,2052,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 06 GCCAAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GCCAAT,RPI -,1218,2053,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 07 CAGATC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAGATC,RPI -,1219,2054,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 08 ACTTGA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACTTGA,RPI -,1220,2056,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 10 TAGCTT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,TAGCTT,RPI -,1221,Serum_0103,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 34 CATGGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CATGGC,RPI -,1222,Granulocytes,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 31 CACGAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CACGAT,RPI -,1223,H2O,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 11 GGCTAC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GGCTAC,RPI -,1224,T07_16098,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 13 AGTCAA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,AGTCAA,RPI -,1225,T07_17332,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 14 AGTTCC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,AGTTCC,RPI -,1226,T08_0617,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 15 ATGTCA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATGTCA,RPI -,1227,T06_16822,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 16 CCGTCC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CCGTCC,RPI -,1228,T06_0601,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 17 GTAGAG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTAGAG,RPI -,1229,T03_62818,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 18 GTCCGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTCCGC,RPI -,1230,T02_104821,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 19 GTGAAA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTGAAA,RPI -,1231,T97_13615,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 20 GTGGCC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTGGCC,RPI -,1232,T10_18095,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 21 GTTTCG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTTTCG,RPI -,1233,T09_20721,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 22 CGTACG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CGTACG,RPI -,1234,T09_04104,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 23 GAGTGG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GAGTGG,RPI -,1235,T09_15160,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 24 GGTAGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GGTAGC,RPI -,1236,T08_15966,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 25 ACTGAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACTGAT,RPI -,1237,T05_15373,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 26 ATGAGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATGAGC,RPI -,1238,T07_17380,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 27 ATTCCT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATTCCT,RPI -,1239,T09_15289,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 28 CAAAAG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAAAAG,RPI -,1240,T06_10848,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 29 CAACTA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAACTA,RPI -,1241,T02_01220,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 30 CACCGG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CACCGG,RPI -,1242,n_CD4,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 31 CACGAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CACGAT,RPI -,1243,Granulocytes,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 05 ACAGTG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACAGTG,RPI -,1279,ctr2_tRNA_0h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 973, 50 bp run, pool 14",,121113,SN163,0482,BC1B32ACXX,7,RPI 07 CAGATC,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,CAGATC,RPI -,1280,ctr4_RPF_0h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 974, 50 bp run, pool 14",,121113,SN163,0482,BC1B32ACXX,7,RPI 10 TAGCTT,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,TAGCTT,RPI -,1281,uc1_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 975, 50 bp run, pool 14",,121113,SN163,0482,BC1B32ACXX,7,RPI 21 GTTTCG,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,GTTTCG,RPI -,1282,ctr2_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 953, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 09 GATCAG,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,GATCAG,RPI -,1283,ctr4_tRNA_2h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 954, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 08 ACTTGA,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,ACTTGA,RPI -,1284,ctr5_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 955, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 21 GTTTCG,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,GTTTCG,RPI -,1285,UC2_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 956, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 15 ATGTCA,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,ATGTCA,RPI \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/runlocal.sh b/modules/compute/demo/run0482/compute2/generatedscripts/runlocal.sh deleted file mode 100644 index 05f408d1b0..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/runlocal.sh +++ /dev/null @@ -1,10 +0,0 @@ -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/in-house_workflow_data_archiving_csv.started -export PBS_O_WORKDIR=${DIR} -echo Starting with s00_RunGerald_0482... -sh s00_RunGerald_0482.sh -#Dependencies: - -echo Starting with s01_CopyFqToRawdatadir_0482... -sh s01_CopyFqToRawdatadir_0482.sh -#Dependencies: -W depend=afterok:$s00_RunGerald_0482 diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/s00_RunGerald_0482.sh b/modules/compute/demo/run0482/compute2/generatedscripts/s00_RunGerald_0482.sh deleted file mode 100644 index 111f194571..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/s00_RunGerald_0482.sh +++ /dev/null @@ -1,86 +0,0 @@ -# Configures the GCC bash environment -. /scratch1/gcc.bashrc - -##### BEFORE ##### -touch $PBS_O_WORKDIR/s00_RunGerald_0482.out -source /scratch1/tools/scripts/import.sh -before="$(date +%s)" -echo "Begin job s00_RunGerald_0482 at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### -# This script is processing samples: -# 2048 -# 2049 -# 2050 -# 2051 -# 2055 -# Serum_0102 -# CSF_473 -# H2O -# 2047 -# 2052 -# 2053 -# 2054 -# 2056 -# Serum_0103 -# Granulocytes -# H2O -# T07_16098 -# T07_17332 -# T08_0617 -# T06_16822 -# T06_0601 -# T03_62818 -# T02_104821 -# T97_13615 -# T10_18095 -# T09_20721 -# T09_04104 -# T09_15160 -# T08_15966 -# T05_15373 -# T07_17380 -# T09_15289 -# T06_10848 -# T02_01220 -# n_CD4 -# Granulocytes -# ctr2_tRNA_0h -# ctr4_RPF_0h -# uc1_tRNA_24h -# ctr2_tRNA_24h -# ctr4_tRNA_2h -# ctr5_tRNA_24h -# UC2_tRNA_24h - -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:59:00 mem=12 cores=8 -#FOREACH run - -#Source GAF bash -. /scratch1/gaf.bashrc - - -perl /scratch1/tools/scripts/run_GERALD.pl \ --run 0482 \ --samplecsv /Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/demo/run0482/run0482.csv - -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed s00_RunGerald_0482 at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/s00_RunGerald_0482.finished -######## END ######## - diff --git a/modules/compute/demo/run0482/compute2/generatedscripts/s01_CopyFqToRawdatadir_0482.sh b/modules/compute/demo/run0482/compute2/generatedscripts/s01_CopyFqToRawdatadir_0482.sh deleted file mode 100644 index 6a8b8a186c..0000000000 --- a/modules/compute/demo/run0482/compute2/generatedscripts/s01_CopyFqToRawdatadir_0482.sh +++ /dev/null @@ -1,88 +0,0 @@ -# Configures the GCC bash environment -. /scratch1/gcc.bashrc - -##### BEFORE ##### -touch $PBS_O_WORKDIR/s01_CopyFqToRawdatadir_0482.out -source /scratch1/tools/scripts/import.sh -before="$(date +%s)" -echo "Begin job s01_CopyFqToRawdatadir_0482 at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### -# This script is processing samples: -# 2048 -# 2049 -# 2050 -# 2051 -# 2055 -# Serum_0102 -# CSF_473 -# H2O -# 2047 -# 2052 -# 2053 -# 2054 -# 2056 -# Serum_0103 -# Granulocytes -# H2O -# T07_16098 -# T07_17332 -# T08_0617 -# T06_16822 -# T06_0601 -# T03_62818 -# T02_104821 -# T97_13615 -# T10_18095 -# T09_20721 -# T09_04104 -# T09_15160 -# T08_15966 -# T05_15373 -# T07_17380 -# T09_15289 -# T06_10848 -# T02_01220 -# n_CD4 -# Granulocytes -# ctr2_tRNA_0h -# ctr4_RPF_0h -# uc1_tRNA_24h -# ctr2_tRNA_24h -# ctr4_tRNA_2h -# ctr5_tRNA_24h -# UC2_tRNA_24h - -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. /scratch1/gcc.bashrc - -umask 0007 - -/scratch1/tools/scripts/copy_fq_to_rawdatadir.pl \ --rawdatadir /scratch1/groups/in-house/runs//121113_SN163_0482_BC1B32ACXX/results/ \ --run 0482 \ --samplecsv /Users/mdijkstra/Documents/work/git/molgenis_apps/modules/compute/demo/run0482/run0482.csv - -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed s01_CopyFqToRawdatadir_0482 at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/s01_CopyFqToRawdatadir_0482.finished -######## END ######## - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a.zip b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a.zip deleted file mode 100644 index 1595abb443..0000000000 Binary files a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a.zip and /dev/null differ diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/README_molgenis_compute.txt b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/README_molgenis_compute.txt deleted file mode 100644 index ebdf99d6e4..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/README_molgenis_compute.txt +++ /dev/null @@ -1,52 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# -# README for the MOLGENIS/compute script generator (command line version) -# - -WARNING: Please remove any previous version of molgenis_compute before unzipping a next version. Simply unzipping a new version on top of another version will disable its execution. Reason unknown. - -To run the MOLGENIS/compute script generator - -1. You may want to change the permissions of the script to start MOLGENIS/compute: - - $> chmod 755 molgenis_compute.sh - -2. Simply execute molgenis_compute.sh without parameters to get an up to date listing of command line options: - - $> molgenis_compute.sh - -3. Next Generation Sequencing (NGS) workflow example - - You can generate a Next Generation Sequencing (NGS) workflow for a small test set by executing the following: - - $> sh molgenis_compute.sh \ - -parameters=workflows/in-house_parameters.csv \ - -workflow=workflows/in-house_workflow.csv \ - -worksheet=workflows/in-house_worksheet_test.csv \ - -protocols=protocols \ - -templates=dummy \ - -scripts=scripts \ - -id=run01 - -Please note that: - * White space before and after the '=' is not allowed when specifying the parameters. - * The raw data for the samples described in worksheetTest.csv is not packaged with MOLGENIS/compute, - so you can use worksheetTest.csv to test the generate of job scripts, but you cannot execute those example scripts - successfully without real raw data. - * The -templates param is not functional yet, but you have to specify it anyway (work in progress). - * The last parameter specified (run01 in the example above) is the ID/name of this set of generated scripts. - Choose something that suits your needs. - * All commandline arguments are available as special MOLGENIS/compute parameters, so you can use them in the Freemarker templates for your protocols. - The syntax for these special params: param name starting with a capital and prefixed with Mc. - For example to use the path to the parameters file you specified on the cammandline you can use ${McParameters} in your protocols. - In addition to the commandline arguments there is one more special MOLGENIScompute param "$McDir}, - which points to the dir where MOLGENIS/compute is installed == where molgenis_compute.sh is stored. - -Questions, bug reports or feature requests? Please contact the MOLGENIS/compute developers via gcc-ngs@googlegroups.com or visit http://molgenis.org/. \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/commons-io-2.4.jar b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/commons-io-2.4.jar deleted file mode 100644 index 90035a4fe0..0000000000 Binary files a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/commons-io-2.4.jar and /dev/null differ diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/freemarker.jar b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/freemarker.jar deleted file mode 100644 index 968c1d3149..0000000000 Binary files a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/freemarker.jar and /dev/null differ diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/molgenis-b6e0274.jar b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/molgenis-b6e0274.jar deleted file mode 100644 index 3c54d867c8..0000000000 Binary files a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/molgenis-b6e0274.jar and /dev/null differ diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/molgenis-compute-f6e477a.jar b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/molgenis-compute-f6e477a.jar deleted file mode 100644 index 5c56227828..0000000000 Binary files a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/lib/molgenis-compute-f6e477a.jar and /dev/null differ diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/molgenis_compute.sh b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/molgenis_compute.sh deleted file mode 100644 index 49cd9ff6c3..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/molgenis_compute.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash -# -# This script runs the MOLGENIS/compute commandline with only the jars needed added to the CLASSPATH. -# To get relative path to this script use $(dirname -- "$0"). -# - -MCDIR=$( cd -P "$( dirname "$0" )" && pwd ) - -java -cp \ -$(dirname -- "$0")/lib/molgenis-b6e0274.jar:\ -$(dirname -- "$0")/lib/molgenis-compute-f6e477a.jar:\ -$(dirname -- "$0")/lib/commons-io-2.4.jar:\ -$(dirname -- "$0")/lib/freemarker.jar:\ -$(dirname -- "$0")/lib/log4j-1.2.15.jar \ -org.molgenis.compute.commandline.ComputeCommandLine \ --mcdir=${MCDIR} \ -$* - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/AnalyzeCovariates.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/AnalyzeCovariates.ftl deleted file mode 100644 index b5e242a610..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/AnalyzeCovariates.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:45:00 - -inputs "${matefixedcovariatecsv}" -inputs "${sortedrecalcovariatecsv}" -alloutputsexist \ -"${cyclecovariatebefore}" \ -"${cyclecovariateafter}" - -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -java -jar -Xmx4g ${analyzecovariatesjar} -l INFO \ --resources ${indexfile} \ ---recal_file ${matefixedcovariatecsv} \ --outputDir ${recalstatsbeforedir} \ --Rscript ${rscript} \ --ignoreQ 5 - -java -jar -Xmx4g ${analyzecovariatesjar} -l INFO \ --resources ${indexfile} \ ---recal_file ${sortedrecalcovariatecsv} \ --outputDir ${recalstatsafterdir} \ --Rscript ${rscript} \ --ignoreQ 5 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaAlignLeft.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaAlignLeft.ftl deleted file mode 100644 index 452dfff48b..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaAlignLeft.ftl +++ /dev/null @@ -1,29 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=15:00:00 nodes=1 cores=4 mem=6 - -#INPUTS indexfile,leftbarcodefqgz -#OUTPUTS leftbwaout -#LOGS log -#EXES bwaalignjar -#TARGETS - -inputs "${indexfile}" -inputs "${leftbarcodefqgz}" -alloutputsexist "${leftbwaout}" - -mkdir -p "${intermediatedir}" - -${bwaalignjar} aln \ -${indexfile} \ -${leftbarcodefqgz} \ --t ${bwaaligncores} \ --f ${leftbwaout} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaAlignRight.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaAlignRight.ftl deleted file mode 100644 index 6b918b2df4..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaAlignRight.ftl +++ /dev/null @@ -1,31 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -<#if seqType == "PE"> -#MOLGENIS walltime=15:00:00 nodes=1 cores=4 mem=6 - -#INPUTS indexfile,rightbarcodefqgz -#OUTPUTS rightbwaout -#LOGS log -#EXES bwaalignjar -#TARGETS - -inputs "${indexfile}" -inputs "${rightbarcodefqgz}" -alloutputsexist "${rightbwaout}" - -mkdir -p "${intermediatedir}" - -${bwaalignjar} aln \ -${indexfile} \ -${rightbarcodefqgz} \ --t ${bwaaligncores} \ --f ${rightbwaout} - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaSampe.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaSampe.ftl deleted file mode 100644 index 35bc194bd0..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/BwaSampe.ftl +++ /dev/null @@ -1,36 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=23:59:00 - -#INPUTS indexfile,leftbwaout,rightbwaout,leftbarcodefqgz,rightbarcodefqgz -#OUTPUTS samfile -#LOGS log -#EXES bwasampejar -#TARGETS - -inputs "${indexfile}" -inputs "${leftbwaout}" -inputs "${rightbwaout}" -inputs "${leftbarcodefqgz}" -inputs "${rightbarcodefqgz}" -alloutputsexist "${samfile}" - -<#if seqType == "PE">${bwasampejar} sampe -P \<#else>${bwasampejar} samse \ --p illumina \ --i ${lane} \ --m ${externalSampleID} \ --l ${library} \ -${indexfile} \ -${leftbwaout} \ -<#if seqType == "PE">${rightbwaout} \ -${leftbarcodefqgz} \ -<#if seqType == "PE">${rightbarcodefqgz} \ --f ${samfile} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckMd5SumsRawData.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckMd5SumsRawData.ftl deleted file mode 100644 index 55cf03a375..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckMd5SumsRawData.ftl +++ /dev/null @@ -1,22 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate 28 Jun 2012 $ -# $LastChangedRevision$ -# $LastChangedBy WBKoetsier$ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. ${root}/gcc.bashrc - -umask 0007 - -${gafscripts}/copy_fq_to_rawdatadir.pl \ --rawdatadir ${runIntermediateDir} \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckMd5SumsResults.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckMd5SumsResults.ftl deleted file mode 100644 index f5ab07113b..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckMd5SumsResults.ftl +++ /dev/null @@ -1,22 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. ${root}/gcc.bashrc - -umask 0007 - -${gafscripts}/copy_fq_to_rawdatadir.pl \ --rawdatadir ${runIntermediateDir} \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckRawdataPresence.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckRawdataPresence.ftl deleted file mode 100644 index caa1c94708..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CheckRawdataPresence.ftl +++ /dev/null @@ -1,90 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=1:00:00 nodes=1 cores=1 mem=1 -#FOREACH flowcell, lane, seqType, filenamePrefix - -# -# For each lane. -# -<#if seqType == "SR"> - - # - # Check the complete lane files. - # - ls ${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenameSR} - ls ${allRawNgsDataDir}/${runPrefix}/${fastqChecksumFilenameSR} - - <#if barcode[0] == "None"> - <#else> - # - # Check demultiplexing success. - # - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.read_count_check.passed - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.log - - # - # For the demultiplexed sample FastQ files: - # - <#list demultiplexedSampleFastqFilenameSR as fileToCheck> - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedSampleFastqFilenameSR[fileToCheck_index]} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]} - - - # - # Same for the discarded reads FastQ file. - # - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedDiscardedFastqChecksumFilenameSR} - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedDiscardedFastqFilenameSR} - - - -<#elseif seqType == "PE"> - - # - # Check the complete lane files. - # - ls ${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenamePE1} - ls ${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenamePE2} - ls ${allRawNgsDataDir}/${runPrefix}/${fastqChecksumFilenamePE1} - ls ${allRawNgsDataDir}/${runPrefix}/${fastqChecksumFilenamePE2} - - <#if barcode[0] == "None"> - <#else> - # - # Check demultiplexing success. - # - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.read_count_check.passed - ls ${allRawNgsDataDir}/${runPrefix}/${filenamePrefix}.demultiplex.log - - # - # For the demultiplexed sample FastQ files: - # - <#list demultiplexedSampleFastqFilenamePE1 as fileToCheck> - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedSampleFastqFilenamePE1[fileToCheck_index]} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]} - - <#list demultiplexedSampleFastqFilenamePE2 as fileToCheck> - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedSampleFastqFilenamePE2[fileToCheck_index]} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]} - - - # - # Same for the discarded reads FastQ file. - # - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedDiscardedFastqFilenamePE1} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedDiscardedFastqChecksumFilenamePE1} - - ls ${allRawNgsDataDir}/${runPrefix}/${compressedDemultiplexedDiscardedFastqFilenamePE2} - ls ${allRawNgsDataDir}/${runPrefix}/${demultiplexedDiscardedFastqChecksumFilenamePE2} - - - - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/ConcordanceCheck.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/ConcordanceCheck.ftl deleted file mode 100644 index e3eda944dd..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/ConcordanceCheck.ftl +++ /dev/null @@ -1,359 +0,0 @@ -# -# ===================================================== -# $Id: ConcordanceCheck.ftl 12159 2012-06-13 10:56:41Z freerkvandijk $ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/ConcordanceCheck.ftl $ -# $LastChangedDate: 2012-06-13 12:56:41 +0200 (Wed, 13 Jun 2012) $ -# $LastChangedRevision: 12159 $ -# $LastChangedBy: freerkvandijk $ -# ===================================================== -# - -#MOLGENIS walltime=09:59:00 mem=4 -#FOREACH externalSampleID - -inputs "${mergedbam}" -alloutputsexist \ -"${finalreport}" \ -"${familylist}" \ -"${sample}.concordance.fam" \ -"${sample}.concordance.lgen" \ -"${arraytmpmap}" \ -"${arraymapfile}" \ -"${sample}.ped" \ -"${sample}.genotypeArray.vcf" \ -"${sample}.genotypeArray.bed" \ -"${sample}.genotypeArray.fasta" \ -"${sample}.genotypeArray.aligned_to_ref.vcf.out" \ -"${sample}.genotypeArray.aligned_to_ref.vcf" \ -"${sample}.genotypeArray.aligned_to_ref.lifted_over.vcf" \ -"${sample}.genotypeArray.header.txt" \ -"${sample}.genotypeArray.headerless.vcf" \ -"${sample}.genotypeArray.updated.header.vcf" \ -"${sample}.concordance.allSites.vcf" \ -"${sample}.genotypeArray.updated.header.interval_list" \ -"${sample}.concordance.q20.dp10.vcf" \ -"${sample}.concordance.q20.dp10.eval" \ -"${sampleconcordancefile}" - -if test ! -e ${finalreport}; -then - echo "name, step, nSNPs, PercDbSNP, Ti/Tv_known, Ti/Tv_Novel, All_comp_het_called_het, Known_comp_het_called_het, Non-Ref_Sensitivity, Non-Ref_discrepancy, Overall_concordance" > ${sampleconcordancefile} - echo "[1] NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA" >> ${sampleconcordancefile} -else - ##Set R library path - export PATH=${R_HOME}/bin:<#noparse>${PATH} - export R_LIBS=${R_LIBS} - - ##Push sample belonging to family "1" into list.txt - echo '1 ${externalSampleID}' > ${familylist} - - ######################################################################### - ######################################################################### - ######################################################################### - # Use 'probe positions' to check whether the array file / final report is in build 36 or build 37. - # In some cases the the position is erroneously one too small. In those cases, we add one to all positions in the array file / final report. - - # Load ten rs-ids and positions of ten probes that should be present on build 36 and also on build 37. - # The difference in positions between none of the probes on b36 and b37 is 1. - # Therefore, we can safely test whether a position matches on position n or n+1... - - rs[0]=rs4830576 - b36[0]=8245875 - b37[0]=8285875 - rs[1]=rs922257 - b36[1]=20391000 - b37[1]=20481079 - rs[2]=rs2168861 - b36[2]=31773234 - b37[2]=31863313 - rs[3]=rs5918076 - b36[3]=40718890 - b37[3]=40833946 - rs[4]=rs5936538 - b36[4]=69241401 - b37[4]=69324676 - rs[5]=rs4826938 - b36[5]=105496014 - b37[5]=105609358 - rs[6]=rs2208263 - b36[6]=115330016 - b37[6]=115415988 - rs[7]=rs1279816 - b36[7]=123183295 - b37[7]=123355614 - rs[8]=rs370713 - b36[8]=138470059 - b37[8]=138642393 - rs[9]=rs2266828 - b36[9]=149374751 - b37[9]=149624093 - - # Find out which build was used. This info is stored in $build (build36, build37, N/A, ERROR) - build="N/A" - - # Find out whether we have to increase all positions in the array file with 1. - # Store this in the variable $increase1 ("true", "false") - increase1="false" - - i=0 - unset ready - while [ -z $ready ] - do - position=`awk '$1 == "'<#noparse>${rs[$i]}'" {print $7}' ${finalreport}` - - echo "<#noparse>${rs[$i]} has position <#noparse>${position}" - - # does the probe exist in this file? - if [ ! -z $position ] - then - ready="ready" - - if [ <#noparse>${position//$'\r'} == ${b36[$i]} ] - then - # we are on build 36 - build="build36" - elif [ <#noparse>${position//$'\r'} == ${b37[$i]} ] - then - # we are on build 37 - build="build37" - elif [ <#noparse>$((${position//$'\r'} + 1)) == ${b36[$i]} ] - then - # we are on build 36 (after increasing position with 1) - build="build36" - increase1="true" - elif [ <#noparse>$((${position//$'\r'} + 1)) == ${b37[$i]} ] - then - # we are on build 37 (after increasing position with 1) - build="build37" - increase1="true" - else - # we are neither on build 36 nor on build 37, according to this test - build="ERROR" - fi - fi - - # stop if we have tested all probes - if [ <#noparse>${#rs[@]} -le $(($i+1)) ] - then - ready="ready" - fi - - # increase counter - i=$[$i+1] - done - - # Now copy the array file / final report to the tmp dir - # Or, if increase1 == "true" then use awk to add one to the positions and redirect standard out to tmp dir - - if [ $increase1 == "false" ] - then - cp ${finalreport} ${finalreporttmpdir} - elif [ $increase1 == "true" ] - then - awk '{$7=$7+1; print $1,$2,$3,$4,$5,$6,$7}' OFS="\t" ${finalreport} > ${finalreporttmpdir} - else - echo "ERROR, variable increase1 should be either false or true" - fi - - - ######################################################################### - ######################################################################### - ######################################################################### - - ##Create .fam, .lgen and .map file from sample_report.txt - sed -e '1,10d' ${finalreporttmpdir} | awk '{print "1",$2,"0","0","0","1"}' | uniq > ${sample}.concordance.fam - sed -e '1,10d' ${finalreporttmpdir} | awk '{print "1",$2,$1,$3,$4}' | awk -f ${tooldir}/scripts/RecodeFRToZero.awk > ${sample}.concordance.lgen - sed -e '1,10d' ${finalreporttmpdir} | awk '{print $6,$1,"0",$7}' OFS="\t" | sort -k1n -k4n | uniq > ${arraytmpmap} - grep -P '^[123456789]' ${arraytmpmap} | sort -k1n -k4n > ${arraymapfile} - grep -P '^[X]\s' ${arraytmpmap} | sort -k4n >> ${arraymapfile} - grep -P '^[Y]\s' ${arraytmpmap} | sort -k4n >> ${arraymapfile} - - #?# MD vraagt: wat doen --lfile en --out, en horen die gelijk te zijn? - ##Create .bed and other files (keep sample from sample_list.txt). - ${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink \ - --lfile ${sample}.concordance \ - --recode \ - --out ${sample}.concordance \ - --keep ${familylist} - - ##Create genotype VCF for sample - ${tooldir}/plink-1.08/plink108 \ - --recode-vcf \ - --ped ${sample}.concordance.ped \ - --map ${arraymapfile} \ - --out ${sample}.concordance - - ##Rename plink.vcf to sample.vcf - mv ${sample}.concordance.vcf ${sample}.genotypeArray.vcf - - ##Replace chr23 and 24 with X and Y - perl -pi -e 's/^23/X/' ${sample}.genotypeArray.vcf - perl -pi -e 's/^24/Y/' ${sample}.genotypeArray.vcf - - ##Remove family ID from sample in header genotype VCF - perl -pi -e 's/1_${externalSampleID}/${externalSampleID}/' ${sample}.genotypeArray.vcf - - ##Create binary ped (.bed) and make tab-delimited .fasta file for all genotypes - sed -e 's/chr//' ${sample}.genotypeArray.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2}}' \ - > ${sample}.genotypeArray.bed - - ${tooldir}/BEDTools-Version-2.11.2/bin/fastaFromBed \ - -fi ${resdir}/b36/hs_ref_b36.fasta \ - -bed ${sample}.genotypeArray.bed \ - -fo ${sample}.genotypeArray.fasta -tab - - - #################################### - if [ $build == "build36" ] - then # File is on build36 - - ##Align vcf to reference AND DO NOT FLIP STRANDS!!! (genotype data is already in forward-forward format) If flipping is needed use "-f" command before sample.genotype_array.vcf - perl ${tooldir}/scripts/align-vcf-to-ref.pl \ - ${sample}.genotypeArray.vcf \ - ${sample}.genotypeArray.fasta \ - ${sample}.genotypeArray.aligned_to_ref.vcf \ - > ${sample}.genotypeArray.aligned_to_ref.vcf.out - - ##Lift over sample.genotype_array.aligned_to_ref.vcf from build 36 to build 37 - perl ${tooldir}/GATK-1.0.5069/Sting/perl/liftOverVCF.pl \ - -vcf ${sample}.genotypeArray.aligned_to_ref.vcf \ - -gatk ${tooldir}/GATK-1.0.5069/Sting \ - -chain ${resdir}/b36/chainfiles/b36ToHg19.broad.over.chain \ - -newRef ${resdir}/hg19/indices/human_g1k_v37 \ - -oldRef ${resdir}/b36/hs_ref_b36 \ - -tmp ${tempdir} \ - -out ${sample}.genotypeArray.aligned_to_ref.lifted_over.vcf - - ##Some GATK versions sort header alphabetically, which results in wrong individual genotypes. So cut header from "original" sample.genotype_array.vcf and replace in sample.genotype_array.aligned_to_ref.lifted_over.out - head -3 ${sample}.genotypeArray.vcf > ${sample}.genotypeArray.header.txt - - sed '1,4d' ${sample}.genotypeArray.aligned_to_ref.lifted_over.vcf \ - > ${sample}.genotypeArray.headerless.vcf - - cat ${sample}.genotypeArray.header.txt \ - ${sample}.genotypeArray.headerless.vcf \ - > ${sample}.genotypeArray.updated.header.vcf - - ##Create interval_list of CHIP SNPs to call SNPs in sequence data on - perl ${tooldir}/scripts/iChip_pos_to_interval_list.pl \ - ${sample}.genotypeArray.updated.header.vcf \ - ${sample}.genotypeArray.updated.header.interval_list - - ###THESE STEPS USE NEWER VERSION OF GATK THAN OTHER STEPS IN ANALYSIS PIPELINE!!! - ##Call SNPs on all positions known to be on array and output VCF (including hom ref calls) - java -Xmx4g -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -l INFO \ - -T UnifiedGenotyper \ - -R ${indexfile} \ - -I ${mergedbam} \ - -o ${sample}.concordance.allSites.vcf \ - -stand_call_conf 30.0 \ - -stand_emit_conf 10.0 \ - -out_mode EMIT_ALL_SITES \ - -L ${sample}.genotypeArray.updated.header.interval_list - - ##Change FILTER column from GATK "called SNPs". All SNPs having Q20 & DP10 change to "PASS", all other SNPs are "filtered" (not used in concordance check) - perl ${tooldir}/scripts/change_vcf_filter.pl \ - ${sample}.concordance.allSites.vcf \ - ${sample}.concordance.q20.dp10.vcf 10 20 - - ##Calculate condordance between genotype SNPs and GATK "called SNPs" - java -Xmx2g -Djava.io.tmpdir=${tempdir} -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -T VariantEval \ - -eval:eval,VCF ${sample}.concordance.q20.dp10.vcf \ - -comp:comp_immuno,VCF ${sample}.genotypeArray.updated.header.vcf \ - -o ${sample}.concordance.q20.dp10.eval \ - -R ${indexfile} \ - -D:dbSNP,VCF ${dbsnpexsitesafter129vcf} \ - -EV GenotypeConcordance - - ##Create concordance output file with header - echo 'name, step, nSNPs, PercDbSNP, Ti/Tv_known, Ti/Tv_Novel, All_comp_het_called_het, Known_comp_het_called_het, Non-Ref_Sensitivity, Non-Ref_discrepancy, Overall_concordance' \ - > ${sampleconcordancefile} - - ##Retrieve name,step,#SNPs,%dbSNP,Ti/Tv known,Ti/Tv Novel,Non-Ref Sensitivity,Non-Ref discrepancy,Overall concordance from sample.q20_dp10_concordance.eval - ##Don't forget to add .libPaths("/target/gpfs2/gcc/tools/GATK-1.3-24-gc8b1c92/public/R") to your ~/.Rprofile - Rscript ${tooldir}/scripts/extract_info_GATK_variantEval_V3.R \ - --in ${sample}.concordance.q20.dp10.eval \ - --step q20_dp10_concordance \ - --name ${externalSampleID} \ - --comp comp_immuno \ - --header >> ${sampleconcordancefile} - fi - if [ $build == "build37" ] - then - ################################### - #Arrayfile is on build 37 - - ##Align vcf to reference AND DO NOT FLIP STRANDS!!! (genotype data is already in forward-forward format) If flipping is needed use "-f" command before sample.genotype_array.vcf - perl ${tooldir}/scripts/align-vcf-to-ref.pl \ - ${sample}.genotypeArray.vcf \ - ${sample}.genotypeArray.fasta \ - ${sample}.genotypeArray.aligned_to_ref.vcf \ - > ${sample}.genotypeArray.aligned_to_ref.vcf.out - - ##Some GATK versions sort header alphabetically, which results in wrong individual genotypes. So cut header from "original" sample.genotype_array.vcf and replace in sample.genotype_array.aligned_to_ref.lifted_over.out - head -3 ${sample}.genotypeArray.vcf > ${sample}.genotypeArray.header.txt - - sed '1,3d' ${sample}.genotypeArray.aligned_to_ref.vcf \ - > ${sample}.genotypeArray.headerless.vcf - - cat ${sample}.genotypeArray.header.txt \ - ${sample}.genotypeArray.headerless.vcf \ - > ${sample}.genotypeArray.updated.header.vcf - - ##Create interval_list of CHIP SNPs to call SNPs in sequence data on - perl ${tooldir}/scripts/iChip_pos_to_interval_list.pl \ - ${sample}.genotypeArray.updated.header.vcf \ - ${sample}.genotypeArray.updated.header.interval_list - - ###THESE STEPS USE NEWER VERSION OF GATK THAN OTHER STEPS IN ANALYSIS PIPELINE!!! - ##Call SNPs on all positions known to be on array and output VCF (including hom ref calls) - java -Xmx4g -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -l INFO \ - -T UnifiedGenotyper \ - -R ${indexfile} \ - -I ${mergedbam} \ - -o ${sample}.concordance.allSites.vcf \ - -stand_call_conf 30.0 \ - -stand_emit_conf 10.0 \ - -out_mode EMIT_ALL_SITES \ - -L ${sample}.genotypeArray.updated.header.interval_list - - ##Change FILTER column from GATK "called SNPs". All SNPs having Q20 & DP10 change to "PASS", all other SNPs are "filtered" (not used in concordance check) - perl ${tooldir}/scripts/change_vcf_filter.pl \ - ${sample}.concordance.allSites.vcf \ - ${sample}.concordance.q20.dp10.vcf 10 20 - - ##Calculate condordance between genotype SNPs and GATK "called SNPs" - java -Xmx2g -Djava.io.tmpdir=${tempdir} -jar ${tooldir}/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar \ - -T VariantEval \ - -eval:eval,VCF ${sample}.concordance.q20.dp10.vcf \ - -comp:comp_immuno,VCF ${sample}.genotypeArray.updated.header.vcf \ - -o ${sample}.concordance.q20.dp10.eval \ - -R ${indexfile} \ - -D:dbSNP,VCF ${dbsnpexsitesafter129vcf} \ - -EV GenotypeConcordance - - ##Create concordance output file with header - echo 'name, step, nSNPs, PercDbSNP, Ti/Tv_known, Ti/Tv_Novel, All_comp_het_called_het, Known_comp_het_called_het, Non-Ref_Sensitivity, Non-Ref_discrepancy, Overall_concordance' \ - > ${sampleconcordancefile} - - ##Retrieve name,step,#SNPs,%dbSNP,Ti/Tv known,Ti/Tv Novel,Non-Ref Sensitivity,Non-Ref discrepancy,Overall concordance from sample.q20_dp10_concordance.eval - ##Don't forget to add .libPaths("/target/gpfs2/gcc/tools/GATK-1.3-24-gc8b1c92/public/R") to your ~/.Rprofile - Rscript ${tooldir}/scripts/extract_info_GATK_variantEval_V3.R \ - --in ${sample}.concordance.q20.dp10.eval \ - --step q20_dp10_concordance \ - --name ${externalSampleID} \ - --comp comp_immuno \ - --header >> ${sampleconcordancefile} - fi - if [ $build == "N/A" ] - then - echo "ERROR: unsure which build was used. None of the probes we checked was found in the array file." - fi - if [ $build == "ERROR" ] - then - echo "ERROR: one of the probe in the array file has an unexpected position. Therefore, we are not able to tell which build was used." - fi -fi \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyFqToRawdatadir.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyFqToRawdatadir.ftl deleted file mode 100644 index a8380f147e..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyFqToRawdatadir.ftl +++ /dev/null @@ -1,22 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. ${root}/gcc.bashrc - -umask 0007 - -${gafscripts}/copy_fq_to_rawdatadir.pl \ --rawdatadir ${runResultsDir} \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyFqToResultsDirREADMEtemplate.tex b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyFqToResultsDirREADMEtemplate.tex deleted file mode 100644 index 3434a8a345..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyFqToResultsDirREADMEtemplate.tex +++ /dev/null @@ -1,90 +0,0 @@ -\documentclass[a4paper,12pt]{article} -\usepackage{nameref} -\usepackage{grffile} -\usepackage{graphicx} -\usepackage[strings]{underscore} -\usepackage{verbatim} -\usepackage{wrapfig} -\usepackage{lastpage} - -\begin{comment} -# -# ===================================================== -# $Id: QCReportTemplate.tex 11716 2012-04-20 11:55:31Z mdijkstra $ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/QCReportTemplate.tex $ -# $LastChangedDate: 2012-04-20 13:55:31 +0200 (Fri, 20 Apr 2012) $ -# $LastChangedRevision: 11716 $ -# $LastChangedBy: mdijkstra $ -# ===================================================== -# -\end{comment} - -\newenvironment{narrow}[2]{ - \begin{list}{}{ - \setlength{\leftmargin}{#1} - \setlength{\rightmargin}{#2} - \setlength{\listparindent}{\parindent} - \setlength{\itemindent}{\parindent} - \setlength{\parsep}{\parskip} - } - \item[] -}{\end{list}} - - -\begin{document} -\thispagestyle{empty} -\vspace{40mm} - - -\clearpage -\section*{README} - -This zip file contains the following files and directories: -\subsection*{SNPs} -*.snps.final.vcf = All SNP calls in VCF format. (eg. to be used for Cartagenia etc.) - -\noindent*.snps.final.vcf.table = All SNP calls in tab-delimited format. - -\subsection*{QC} -*_fastqc.zip = Information about the quality of the raw sequence reads. Please read the FastQC manual page for detailed information. - -\#\#\#OPTIONAL\#\#\# - -\noindent*.genotypeArray.updated.header.vcf = Sample genotype calls in VCF format. - - -\subsection*{QC/statistics} -*metric files = Metrics used to compile the QC report. For information/documentation about all metrics not explained in the QC report we refer to the Picard documentation. - - -\subsection*{} - - -${project}.csv = This file contains all the information for the project. If samples were pooled information about the used barcodes etc. can be found here. - -\noindent ${project}_QCReport.pdf = QC report containing all important QC metrics per sample. - - -\subsection*{} - - -\subsection*{Additional files} - -*.merged.bam = The BAM file containing all (un)aligned reads after removing duplicates and quality score recalibration. -This is the final alignment on which SNP calling was executed. - -\noindent*.merged.bam.bai = The index file of the *.merged.bam. - -\noindent*.fq.gz = gzipped FASTQ file containing all reads, if multiple samples were pooled these files contain the demultiplexed reads per flowcell, lane, barcode combination. The exact combination for each sample can be found in the ${project}.csv file. - -\noindent*.fq.md5 = the md5sum for the corresponding FASTQ file. - - -\subsection*{} - - -\section*{Documentation} -FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ -Picard: http://picard.sourceforge.net/picard-metric-definitions.shtml - -\end{document} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyToResultsDir.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyToResultsDir.ftl deleted file mode 100644 index 42d0b3a8b9..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyToResultsDir.ftl +++ /dev/null @@ -1,124 +0,0 @@ -# -# ===================================================== -# $Id: CopyToResultsDir.ftl 12202 2012-06-15 09:10:27Z freerkvandijk $ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/CopyToResultsDir.ftl $ -# $LastChangedDate: 2012-06-15 11:10:27 +0200 (Fri, 15 Jun 2012) $ -# $LastChangedRevision: 12202 $ -# $LastChangedBy: freerkvandijk $ -# ===================================================== -# - -#MOLGENIS walltime=23:59:00 -#FOREACH project - - -alloutputsexist "${projectResultsDir}/${project}.zip" - -# Change permissions - -umask 0007 - - -# Make result directories -mkdir -p ${projectResultsDir}/rawdata -mkdir -p ${projectResultsDir}/alignment -mkdir -p ${projectResultsDir}/coverage -mkdir -p ${projectResultsDir}/snps -mkdir -p ${projectResultsDir}/qc/statistics - - -# Copy error, out and finished logs to project jobs directory - -cp ${projectJobsDir}/*.out ${projectLogsDir} -cp ${projectJobsDir}/*.err ${projectLogsDir} -cp ${projectJobsDir}/*.log ${projectLogsDir} - -# Copy project csv file to project results directory - -cp ${projectJobsDir}/${project}.csv ${projectResultsDir} - - -# Create symlinks for all fastq and md5 files to the project results directory - -cp -rs ${projectrawdatadir} ${projectResultsDir}/rawdata - - -# Copy fastQC output to results directory -cp ${intermediatedir}/*_fastqc.zip ${projectResultsDir}/qc - - -# Copy dedup metrics to results directory -cp ${intermediatedir}/*.dedup.metrics ${projectResultsDir}/qc/statistics - - -# Create md5 sum and copy merged BAM plus index plus md5 sum to results directory -<#if 0 < mergedbam?size> - <#list 0..(mergedbam?size-1) as index> - md5sum ${mergedbam[index]} > ${mergedbam[index]}.md5 - md5sum ${mergedbamindex[index]} > ${mergedbamindex[index]}.md5 - cp ${mergedbam[index]}* ${projectResultsDir}/alignment - - - -# Copy alignment stats (lane and sample) to results directory - -cp ${intermediatedir}/*.alignmentmetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.gcbiasmetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.insertsizemetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.meanqualitybycycle ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.qualityscoredistribution ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.hsmetrics ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.bamindexstats ${projectResultsDir}/qc/statistics -cp ${intermediatedir}/*.pdf ${projectResultsDir}/qc/statistics - - -# Copy coverage stats (for future reference) to results directory - -cp ${intermediatedir}/*.coverage* ${projectResultsDir}/coverage - - -# Copy final vcf and vcf.table to results directory - -<#list sample as s> - - cp ${s}.snps.final.vcf ${projectResultsDir}/snps - cp ${s}.snps.final.vcf.table ${projectResultsDir}/snps - - - # Copy genotype array vcf to results directory - - if [ -f "${s}.genotypeArray.updated.header.vcf" ] - then - cp ${s}.genotypeArray.updated.header.vcf ${projectResultsDir}/qc - fi - - cp ${s}.concordance.ngsVSarray.txt ${projectResultsDir}/qc - - - -# Copy QC report to results directory - -cp ${qcdir}/${project}_QCReport.pdf ${projectResultsDir} - - -# save latex README template in file -echo "<#include "CopyToResultsDirREADMEtemplate.tex"/>" > ${projectResultsDir}/README.txt - -pdflatex -output-directory=${projectResultsDir} ${projectResultsDir}/README.txt - - -# Create zip file for all "small text" files - -cd ${projectResultsDir} - -zip -r ${projectResultsDir}/${project}.zip snps -zip -gr ${projectResultsDir}/${project}.zip qc -zip -g ${projectResultsDir}/${project}.zip ${project}.csv -zip -g ${projectResultsDir}/${project}.zip README.pdf -zip -g ${projectResultsDir}/${project}.zip ${project}_QCReport.pdf - -# Create md5sum for zip file - -cd ${projectResultsDir} - -md5sum ${project}.zip > ${projectResultsDir}/${project}.zip.md5 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyToResultsDirREADMEtemplate.tex b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyToResultsDirREADMEtemplate.tex deleted file mode 100644 index 9c3af69aeb..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CopyToResultsDirREADMEtemplate.tex +++ /dev/null @@ -1,90 +0,0 @@ -\documentclass[a4paper,12pt]{article} -\usepackage{nameref} -\usepackage{grffile} -\usepackage{graphicx} -\usepackage[strings]{underscore} -\usepackage{verbatim} -\usepackage{wrapfig} -\usepackage{lastpage} - -\begin{comment} -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# -\end{comment} - -\newenvironment{narrow}[2]{ - \begin{list}{}{ - \setlength{\leftmargin}{#1} - \setlength{\rightmargin}{#2} - \setlength{\listparindent}{\parindent} - \setlength{\itemindent}{\parindent} - \setlength{\parsep}{\parskip} - } - \item[] -}{\end{list}} - - -\begin{document} -\thispagestyle{empty} -\vspace{40mm} - - -\clearpage -\section*{README} - -This zip file contains the following files and directories: -\subsection*{SNPs} -*.snps.final.vcf = All SNP calls in VCF format. (eg. to be used for Cartagenia etc.) - -\noindent*.snps.final.vcf.table = All SNP calls in tab-delimited format. - -\subsection*{QC} -*_fastqc.zip = Information about the quality of the raw sequence reads. Please read the FastQC manual page for detailed information. - -\#\#\#OPTIONAL\#\#\# - -\noindent*.genotypeArray.updated.header.vcf = Sample genotype calls in VCF format. - - -\subsection*{QC/statistics} -*metric files = Metrics used to compile the QC report. For information/documentation about all metrics not explained in the QC report we refer to the Picard documentation. - - -\subsection*{} - - -${project}.csv = This file contains all the information for the project. If samples were pooled information about the used barcodes etc. can be found here. - -\noindent ${project}_QCReport.pdf = QC report containing all important QC metrics per sample. - - -\subsection*{} - - -\subsection*{Additional files} - -*.merged.bam = The BAM file containing all (un)aligned reads after removing duplicates and quality score recalibration. -This is the final alignment on which SNP calling was executed. - -\noindent*.merged.bam.bai = The index file of the *.merged.bam. - -\noindent*.fq.gz = gzipped FASTQ file containing all reads, if multiple samples were pooled these files contain the demultiplexed reads per flowcell, lane, barcode combination. The exact combination for each sample can be found in the ${project}.csv file. - -\noindent*.fq.md5 = the md5sum for the corresponding FASTQ file. - - -\subsection*{} - - -\section*{Documentation} -FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ -Picard: http://picard.sourceforge.net/picard-metric-definitions.shtml - -\end{document} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Covariates.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Covariates.ftl deleted file mode 100644 index 3ec1209a94..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Covariates.ftl +++ /dev/null @@ -1,27 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -inputs "${matefixedbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -alloutputsexist "${matefixedcovariatecsv}" - -java -jar -Xmx4g \ -${genomeAnalysisTKjar} -l INFO \ --T CountCovariates \ --U ALLOW_UNINDEXED_BAM \ --R ${indexfile} \ ---DBSNP ${dbsnprod} \ --I ${matefixedbam} \ --cov ReadGroupcovariate \ --cov QualityScoreCovariate \ --cov CycleCovariate \ --cov DinucCovariate \ --recalFile ${matefixedcovariatecsv} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CovariatesAfter.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CovariatesAfter.ftl deleted file mode 100644 index cf4d8616c2..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CovariatesAfter.ftl +++ /dev/null @@ -1,11 +0,0 @@ -#MOLGENIS walltime=66:00:00 - -###### Renaming because we call another protocol: - -#input: -<#assign matefixedbam=sortedrecalbam /> - -#output: -<#assign matefixedcovariatecsv=sortedrecalcovariatecsv /> - -<#include "Covariates.ftl" /> diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CovariatesBefore.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CovariatesBefore.ftl deleted file mode 100644 index 3bdc72cadc..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CovariatesBefore.ftl +++ /dev/null @@ -1,3 +0,0 @@ -#MOLGENIS walltime=66:00:00 - -<#include "Covariates.ftl" /> diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Coverage.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Coverage.ftl deleted file mode 100644 index 9fc45a6bf3..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Coverage.ftl +++ /dev/null @@ -1,28 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=65:59:00 mem=12 cores=1 -#FOREACH externalSampleID - -inputs "${mergedbam}" -alloutputsexist "${sample}.coverage.csv" \ -"${samplecoverageplotpdf}" \ -"${sample}.coverage.Rdata" - -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -Rscript ${coveragescript} \ ---bam ${mergedbam} \ ---chromosome 1 \ ---interval_list ${targetintervals} \ ---csv ${sample}.coverage.csv \ ---pdf ${samplecoverageplotpdf} \ ---Rcovlist ${sample}.coverage.Rdata diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CoverageGATK.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CoverageGATK.ftl deleted file mode 100644 index 34480bfdaf..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CoverageGATK.ftl +++ /dev/null @@ -1,43 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=66:00:00 nodes=1 cores=1 mem=12 -#FOREACH externalSampleID - -inputs "${mergedbam}" "${mergedbamindex}" "${indexfile}" -<#if capturingKit != "None">inputs "${targetintervals}" -alloutputsexist "${coveragegatk}" \ -"${coveragegatk}.sample_cumulative_coverage_counts" \ -"${coveragegatk}.sample_cumulative_coverage_proportions" \ -"${coveragegatk}.sample_interval_statistics" \ -"${coveragegatk}.sample_interval_summary" \ -"${coveragegatk}.sample_statistics" \ -"${coveragegatk}.sample_summary" \ -"${coveragegatk}.cumulative_coverage.pdf" - -export PATH=${JAVA_HOME}/bin:<#noparse>${PATH} -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -java -Djava.io.tmpdir=${tempdir} -Xmx12g -jar \ -${genomeAnalysisTKjar} \ --T DepthOfCoverage \ --R ${indexfile} \ --I ${mergedbam} \ --o ${coveragegatk} \ --ct 1 -ct 2 -ct 5 -ct 10 -ct 15 -ct 20 -ct 30 -ct 40 -ct 50<#if capturingKit != "None"> \ --L ${targetintervals} - -#Create coverage graphs for sample -${rscript} ${cumcoveragescriptgatk} \ ---in ${coveragegatk}.sample_cumulative_coverage_proportions \ ---out ${coveragegatk}.cumulative_coverage.pdf \ ---max-depth 100 \ ---title "Cumulative coverage ${externalSampleID}" diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateFinalReport.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateFinalReport.ftl deleted file mode 100644 index 1601b0fa90..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateFinalReport.ftl +++ /dev/null @@ -1,25 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/Recalibrate.ftl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: mdijkstra $ -# ===================================================== -# - -#MOLGENIS walltime=47:59:00 mem=2 cores=1 -#FOREACH run - -#Source GCC bash -. ${root}/gcc.bashrc - -umask 0007 - - - -perl ${scriptdir}/create_per_sample_finalreport.pl \ --inputdir ${arraydir} \ --outputdir ${arraydir} \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateInhouseProjects.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateInhouseProjects.ftl deleted file mode 100644 index 2ee90d444e..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateInhouseProjects.ftl +++ /dev/null @@ -1,88 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:10:00 -#FOREACH project - -# -# Change permissions. -# -umask 0007 - -# -# Create project dirs. -# -mkdir -p ${projectrawarraydatadir} -mkdir -p ${projectrawdatadir} -mkdir -p ${projectJobsDir} -mkdir -p ${projectLogsDir} -mkdir -p ${intermediatedir} -mkdir -p ${projectResultsDir} -mkdir -p ${qcdir} - -# -# Create symlinks to the raw data required to analyse this project -# -# For each sequence file (could be multiple per sample): -# -<#list internalSampleID as sample> - - <#if seqType[sample_index] == "SR"> - - <#if barcode[sample_index] == "None"> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenameSR[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${fastqChecksumFilenameSR[sample_index]} ${projectrawdatadir}/ - <#else> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedDemultiplexedSampleFastqFilenameSR[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${demultiplexedSampleFastqChecksumFilenameSR} ${projectrawdatadir}/ - - - <#elseif seqType[sample_index] == "PE"> - - <#if barcode[sample_index] == "None"> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenamePE1[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedFastqFilenamePE2[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${fastqChecksumFilenamePE1[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${fastqChecksumFilenamePE2[sample_index]} ${projectrawdatadir}/ - <#else> - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedDemultiplexedSampleFastqFilenamePE1[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${compressedDemultiplexedSampleFastqFilenamePE2[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${demultiplexedSampleFastqChecksumFilenamePE1[sample_index]} ${projectrawdatadir}/ - ln -s ${allRawNgsDataDir}/${runPrefix[sample_index]}/${demultiplexedSampleFastqChecksumFilenamePE2[sample_index]} ${projectrawdatadir}/ - - - - - - -# -# TODO: array for each sample: -# - -# -# Create subset of samples for this project. -# -<#--<#assign unfolded = unfoldParametersCSV(parameters) /> -<#list unfolded as sampleSequenceDetails> -echo ${sampleSequenceDetails} >> ${projectJobsDir}/${project}.csv ---> -${scriptdir}/extract_samples_from_GAF_list.pl --i ${McWorksheet} --o ${projectJobsDir}/${project}.csv --c project --q ${project} - -# -# Execute MOLGENIS/compute to create job scripts to analyse this project. -# -sh ${McDir}/molgenis_compute.sh \ --worksheet=${projectJobsDir}/${project}.csv \ --parameters=${McParameters} \ --workflow=${workflowFile} \ --protocols=${McProtocols}/ \ --templates=${McTemplates}/ \ --scripts=${projectJobsDir}/ \ --id=${McId} diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateInhouseRuns.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateInhouseRuns.ftl deleted file mode 100644 index 692e85fc62..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CreateInhouseRuns.ftl +++ /dev/null @@ -1,44 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:10:00 -#FOREACH run, flowcell - -# -# Change permissions. -# -umask 0007 - -# -# Create run dirs. -# -mkdir -p ${runJobsDir} -mkdir -p ${runResultsDir} - -# -# Create subset of samples for this project. -# -<#--<#assign unfolded = unfoldParametersCSV(parameters) /> -<#list unfolded as sampleSequenceDetails> -echo ${sampleSequenceDetails} >> ${runJobsDir}/${run}.csv ---> -${scriptdir}/extract_samples_from_GAF_list.pl --i ${McWorksheet} --o ${runJobsDir}/${run}.csv --c run --q ${run} - -# -# Execute MOLGENIS/compute to create job scripts to analyse this project. -# -sh ${McDir}/molgenis_compute.sh \ --worksheet=${runJobsDir}/${run}.csv \ --parameters=${McParameters} \ --workflow=${demultiplexWorkflowFile} \ --protocols=${McProtocols}/ \ --templates=${McTemplates}/ \ --scripts=${runJobsDir}/ \ --id=${McId} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CustomSubmit.sh.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Demultiplex.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Demultiplex.ftl deleted file mode 100644 index 19c5396587..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Demultiplex.ftl +++ /dev/null @@ -1,229 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=48:00:00 nodes=1 cores=4 mem=1 -#FOREACH flowcell, lane, seqType, filenamePrefix - -export PATH=${R_HOME}/bin:<#noparse>${PATH} - -# -# Check if we need to run this step or wether demultiplexing was already executed successfully in a previous run. -# -# Note: we don't check for presence of the actual demultiplexed reads, but for empty file indicating successfull demultipxing instead -# where success is based on a comparison of the amount of reads in the multiplexed input file and the total amount of reads in -# the demultiplexed output files: these counts should be the same. -# -alloutputsexist "${runResultsDir}/demultiplex.${filenamePrefix}.read_count_check.passed" - -# -# For each lane demultiplex rawdata. -# -<#if seqType == "SR"> - - <#if barcode[0] == "None"> - # - # Do nothing. - # - touch ${runResultsDir}/demultiplex.read_count_check.skipped - <#else> - # - # Check if the files required for demultiplexing are present. - # - #inputs "${allRawNgsDataDir}/${runPrefix}/${compressedFastqFilenameSR}" - inputs "${runResultsDir}/${compressedFastqFilenameSR}" - - # - # Read count of the input file. - # Note: we actually count lines, which equals reads * 4 for FastQ files. - # - reads_in_1=$(gzip -cd ${runResultsDir}/${compressedFastqFilenameSR} | wc -l) - - # - # Demultiplex the multiplexed, gzipped FastQ file. - # - Rscript ${demultiplexscript} --bcs '${csv(barcode)}' \ - --mpr1 ${runResultsDir}/${compressedFastqFilenameSR} \ - --dmr1 '${csv(compressedDemultiplexedSampleFastqFilepathSR)}' \ - --ukr1 ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenameSR} \ - --tm MP \ - > ${runResultsDir}/${filenamePrefix}.demultiplex.log - - # - # Read count of the output file. - # - summed_reads_out_1=0 - - # - # For the demultiplexed, uncompressed FastQ files: - # 1. Calculate MD5Sums. - # 2. Count the amount of lines(, which equals to reads * 4) per file. - # 3. Update the sum of lines of all files. - # - <#list demultiplexedSampleFastqFilenameSR as fileToCheck> - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe - md5sum <${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe | \ - sed 's/ -/ ${fileToCheck}/' > ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR[fileToCheck_index]} | \ - tee ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenameSR[fileToCheck_index]}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - - - # - # Same for the discarded, uncompressed FastQ file. - # - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe - md5sum <${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe | \ - sed 's/ -/ ${demultiplexedDiscardedFastqFilenameSR}/' > ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenameSR} | \ - tee ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenameSR}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - # - # Flush disk caches to disk to make sure we don't loose any demultiplexed data - # when a machine crashes and some of the "written" data was in a write buffer. - # - sync - - # - # Read count sanity check. - # - if (( $reads_in_1 == $summed_reads_out_1 )) - then touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.passed - else touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.FAILED - fi - - - -<#elseif seqType == "PE"> - - <#if barcode[0] == "None"> - # - # Do nothing. - # - touch ${runResultsDir}/demultiplex.read_count_check.skipped - <#else> - # - # Check if the files required for demultiplexing are present. - # - inputs "${runResultsDir}/${compressedFastqFilenamePE1}" - inputs "${runResultsDir}/${compressedFastqFilenamePE2}" - - # - # Read count of the input file. - # Note: we actually count lines, which equals reads * 4 for FastQ files. - # - reads_in_1=$(gzip -cd ${runResultsDir}/${compressedFastqFilenamePE1} | wc -l) - reads_in_2=$(gzip -cd ${runResultsDir}/${compressedFastqFilenamePE2} | wc -l) - - # - # Read count sanity check for the inputs. - # For PE data the amount of reads in both input files must be the same! - # - if (( $reads_in_1 != $reads_in_2)) - then touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.FAILED - echo "FATAL: cannot demultiplex ${filenamePrefix}. Number of reads in both specified PE FastQ input files not the same!" - exit 1 - fi - - # - # Demultiplex the multiplexed, gzipped FastQ file. - # - Rscript ${demultiplexscript} --bcs '${csv(barcode)}' \ - --mpr1 ${runResultsDir}/${compressedFastqFilenamePE1} \ - --mpr2 ${runResultsDir}/${compressedFastqFilenamePE2} \ - --dmr1 '${csv(compressedDemultiplexedSampleFastqFilepathPE1)}' \ - --dmr2 '${csv(compressedDemultiplexedSampleFastqFilepathPE2)}' \ - --ukr1 ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE1} \ - --ukr2 ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE2} \ - --tm MP \ - > ${runResultsDir}/${filenamePrefix}.demultiplex.log - - # - # Read count of the output file. - # - summed_reads_out_1=0 - summed_reads_out_2=0 - - # - # For the demultiplexed, uncompressed FastQ files: - # 1. Calculate MD5Sums. - # 2. Count the amount of lines(, which equals to reads * 4) per file. - # 3. Update the sum of lines of all files. - # - <#list demultiplexedSampleFastqFilenamePE1 as fileToCheck> - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe - md5sum <${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe | \ - sed 's/ -/ ${fileToCheck}/' > ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1[fileToCheck_index]} | \ - tee ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE1[fileToCheck_index]}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - - <#list demultiplexedSampleFastqFilenamePE2 as fileToCheck> - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe - md5sum <${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe | \ - sed 's/ -/ ${fileToCheck}/' > ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2[fileToCheck_index]} | \ - tee ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedSampleFastqChecksumFilenamePE2[fileToCheck_index]}.pipe - summed_reads_out_2=$(( $summed_reads_out_2 + $this_read_count )) - - - # - # Same for the discarded, uncompressed FastQ files. - # - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe - md5sum <${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe | \ - sed 's/ -/ ${demultiplexedDiscardedFastqFilenamePE1}/' > ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE1} | \ - tee ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE1}.pipe - summed_reads_out_1=$(( $summed_reads_out_1 + $this_read_count )) - - this_read_count=0 - mkfifo ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe - md5sum <${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe | \ - sed 's/ -/ ${demultiplexedDiscardedFastqFilenamePE2}/' > ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2} & - this_read_count=$(gzip -cd ${runResultsDir}/${compressedDemultiplexedDiscardedFastqFilenamePE2} | \ - tee ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe | \ - wc -l) - rm ${runResultsDir}/${demultiplexedDiscardedFastqChecksumFilenamePE2}.pipe - summed_reads_out_2=$(( $summed_reads_out_2 + $this_read_count )) - - # - # Flush disk caches to disk to make sure we don't loose any demultiplexed data - # when a machine crashes and some of the "written" data was in a write buffer. - # - sync - - # - # Read count sanity check. - # - if (( $reads_in_1 == $summed_reads_out_1 )) && (( $reads_in_2 == $summed_reads_out_2)) - then touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.passed - else touch ${runResultsDir}/${filenamePrefix}.demultiplex.read_count_check.FAILED - fi - - - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Fastqc.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Fastqc.ftl deleted file mode 100644 index 32e3af1a91..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Fastqc.ftl +++ /dev/null @@ -1,57 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=08:00:00 nodes=1 cores=1 mem=1 - -<#if seqType == "SR"> -#INPUTS srbarcodefqgz, -#OUTPUTS leftfastqczip,leftfastqcsummarytxt,leftfastqcsummarylog -#LOGS log -#EXES fastqcjar -#TARGETS - - inputs "${srbarcodefqgz}" - alloutputsexist \ - "${leftfastqczip}" \ - "${leftfastqcsummarytxt}" \ - "${leftfastqcsummarylog}" \ -<#else> -#INPUTS leftbarcodefqgz,rightbarcodefqgz -#OUTPUTS leftfastqczip,leftfastqcsummarytxt,leftfastqcsummarylog,rightfastqczip,rightfastqcsummarytxt,rightfastqcsummarylog -#LOGS log -#EXES fastqcjar -#TARGETS - - inputs "${leftbarcodefqgz}" - inputs "${rightbarcodefqgz}" - - alloutputsexist \ - "${leftfastqczip}" \ - "${leftfastqcsummarytxt}" \ - "${leftfastqcsummarylog}" \ - "${rightfastqczip}" \ - "${rightfastqcsummarytxt}" \ - "${rightfastqcsummarylog}" - - -# first make logdir... -mkdir -p "${intermediatedir}" - -# pair1 -${fastqcjar} ${leftbarcodefqgz} \ --Dfastqc.output_dir=${intermediatedir} \ --Dfastqc.unzip=false - -<#if seqType == "PE"> -# pair2 -${fastqcjar} ${rightbarcodefqgz} \ --Dfastqc.output_dir=${intermediatedir} \ --Dfastqc.unzip=false - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/FilterIndels.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/FilterIndels.ftl deleted file mode 100644 index 109f59c771..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/FilterIndels.ftl +++ /dev/null @@ -1,22 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=40:00:00 -#FOREACH externalSampleID - -inputs "${indelsbed}" -alloutputsexist "${indelsfilteredbed}" - -perl ${filterSingleSampleCallsperl} \ ---calls ${indelsbed} \ ---max_cons_av_mm 3.0 \ ---max_cons_nqs_av_mm 0.5 \ ---mode ANNOTATE \ -> ${indelsfilteredbed} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Fixmates.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Fixmates.ftl deleted file mode 100644 index 1b191aa031..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Fixmates.ftl +++ /dev/null @@ -1,31 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=6 - -inputs "${realignedbam}" -alloutputsexist \ - "${matefixedbam}" \ - "${matefixedbamindex}" - -java -jar -Xmx6g \ -${fixmateinformationjar} \ -INPUT=${realignedbam} \ -OUTPUT=${matefixedbam} \ -SORT_ORDER=coordinate \ -VALIDATION_STRINGENCY=SILENT \ -TMP_DIR=${tempdir} - -java -jar -Xmx3g ${buildbamindexjar} \ -INPUT=${matefixedbam} \ -OUTPUT=${matefixedbamindex} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Footer.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/GenomicAnnotator.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/GenomicAnnotator.ftl deleted file mode 100644 index 10e4f1bceb..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/GenomicAnnotator.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=24:00:00 mem=10 -#FOREACH externalSampleID - -inputs "${indexfile}" -inputs "${baitsbed}" -inputs "${dbsnpSNPstxt}" -inputs "${snpsvcf}" -alloutputsexist "${snpsgenomicannotatedvcf}" - -#####Annotate with dbSNP135 SNPs only##### -java -Xmx10g -jar ${genomeAnalysisTKjar} \ --T GenomicAnnotator \ --l info \ --R ${indexfile} \ --B:variant,vcf ${snpsvcf} \ --B:dbSNP135,AnnotatorInputTable ${dbsnpSNPstxt} \ --s dbSNP135.AF,dbSNP135.ASP,dbSNP135.ASS,dbSNP135.CDA,dbSNP135.CFL,dbSNP135.CLN,dbSNP135.DSS,dbSNP135.G5,\ -dbSNP135.G5A,dbSNP135.GCF,dbSNP135.GMAF,dbSNP135.GNO,dbSNP135.HD,dbSNP135.INT,dbSNP135.KGPROD,dbSNP135.KGPilot1,dbSNP135.KGPilot123,\ -dbSNP135.KGVAL,dbSNP135.LSD,dbSNP135.MTP,dbSNP135.MUT,dbSNP135.NOC,dbSNP135.NOV,dbSNP135.NS,dbSNP135.NSF,dbSNP135.NSM,dbSNP135.OM,\ -dbSNP135.OTH,dbSNP135.PH1,dbSNP135.PH2,dbSNP135.PH3,dbSNP135.PM,dbSNP135.PMC,dbSNP135.R3,dbSNP135.R5,dbSNP135.REF,dbSNP135.RSPOS,\ -dbSNP135.RV,dbSNP135.S3D,dbSNP135.SAO,dbSNP135.SCS,dbSNP135.SLO,dbSNP135.SSR,dbSNP135.SYN,dbSNP135.TPA,dbSNP135.U3,dbSNP135.U5,dbSNP135.VC,\ -dbSNP135.VLD,dbSNP135.VP,dbSNP135.WGT,dbSNP135.WTD,dbSNP135.dbSNPBuildID \ --o ${snpsgenomicannotatedvcf} \ --L ${baitsbed} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Header.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Header.ftl deleted file mode 100644 index 81962d8cb8..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Header.ftl +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -# Configures the GCC bash environment -. ${root}/gcc.bashrc - -<#include "Macros.ftl"/> -<@begin/> -<#include "NGSHeader.ftl"/> -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Helpers.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/IndelGenotyper.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/IndelGenotyper.ftl deleted file mode 100644 index cf3a6c91b9..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/IndelGenotyper.ftl +++ /dev/null @@ -1,29 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=33:00:00 mem=8 -#FOREACH externalSampleID - -inputs "${mergedbam}" -inputs "${indexfile}" -alloutputsexist \ - "${indelsvcf}" \ - "${indelsbed}" \ - "${indelsverboseoutput}" - -java -Xmx8g -jar ${genomeAnalysisTKjar} \ --l INFO \ --T IndelGenotyperV2 \ --I ${mergedbam} \ --o ${indelsvcf} \ ---bedOutput ${indelsbed} \ --R ${indexfile} \ --verbose ${indelsverboseoutput} \ ---window_size 300 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Macros.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/MakeIndelMask.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/MakeIndelMask.ftl deleted file mode 100644 index bbd3c37d66..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/MakeIndelMask.ftl +++ /dev/null @@ -1,20 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=40:00:00 -#FOREACH externalSampleID - -inputs "${indelsfilteredbed}" -alloutputsexist "${indelsmaskbed}" - -python ${makeIndelMaskpyton} \ -${indelsfilteredbed} \ -10 \ -${indelsmaskbed} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Markduplicates.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Markduplicates.ftl deleted file mode 100644 index 8c1ff6737a..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Markduplicates.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 - -inputs "${sortedbam}" -inputs "${sortedbamindex}" -alloutputsexist \ - "${dedupbam}" \ - "${dedupmetrics}" \ - "${dedupbamindex}" - -java -Xmx4g -jar ${markduplicatesjar} \ -INPUT=${sortedbam} \ -OUTPUT=${dedupbam} \ -METRICS_FILE=${dedupmetrics} \ -REMOVE_DUPLICATES=false \ -ASSUME_SORTED=true \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar -Xmx3g ${buildbamindexjar} \ -INPUT=${dedupbam} \ -OUTPUT=${dedupbamindex} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/MergeBam.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/MergeBam.ftl deleted file mode 100644 index 7b11621714..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/MergeBam.ftl +++ /dev/null @@ -1,35 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=23:59:00 mem=6 cores=2 -#FOREACH externalSampleID - -<#if sortedrecalbam?size == 1> - #cp ${sortedrecalbam[0]} ${mergedbam} - #cp ${sortedrecalbam[0]}.bai ${mergedbamindex} - ln -s ${sortedrecalbam[0]} ${mergedbam} - ln -s ${sortedrecalbam[0]}.bai ${mergedbamindex} -<#else> - java -jar -Xmx6g ${mergesamfilesjar} \ - <#list sortedrecalbam as srb>INPUT=${srb} \ - - ASSUME_SORTED=true USE_THREADING=true \ - TMP_DIR=${tempdir} MAX_RECORDS_IN_RAM=6000000 \ - OUTPUT=${mergedbam} \ - SORT_ORDER=coordinate \ - VALIDATION_STRINGENCY=SILENT - - java -jar -Xmx3g ${buildbamindexjar} \ - INPUT=${mergedbam} \ - OUTPUT=${mergedbamindex} \ - VALIDATION_STRINGENCY=LENIENT \ - MAX_RECORDS_IN_RAM=1000000 \ - TMP_DIR=${tempdir} - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/NGSHeader.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/NGSHeader.ftl deleted file mode 100644 index 23ec161f55..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/NGSHeader.ftl +++ /dev/null @@ -1,6 +0,0 @@ -<#if externalSampleID?exists> -<#if externalSampleID?is_sequence># This script is processing samples: -<#list externalSampleID as sampleToProcess># ${sampleToProcess} - -<#else># This script is processing sample: ${externalSampleID} - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/PicardQC.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/PicardQC.ftl deleted file mode 100644 index 83f20a0233..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/PicardQC.ftl +++ /dev/null @@ -1,104 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 - -inputs "${sortedbam}" -inputs "${indexfile}" -<#if capturingKit != "None"> -inputs ${baitintervals} -inputs ${targetintervals} -#INPUTS sortedbam,indexfile,baitintervals,targetintervals -<#else> -#INPUTS sortedbam,indexfile - - -alloutputsexist \ - "${alignmentmetrics}" \ - "${gcbiasmetrics}" \ - "${gcbiasmetricspdf}" \ - "${insertsizemetrics}" \ - "${insertsizemetricspdf}" \ - "${meanqualitybycycle}" \ - "${meanqualitybycyclepdf}" \ - "${qualityscoredistribution}" \ - "${qualityscoredistributionpdf}" \ - "${hsmetrics}" \ - "${bamindexstats}" - -#OUTPUTS alignmentmetrics,gcbiasmetrics,gcbiasmetricspdf,insertsizemetrics,insertsizemetricspdf,meanqualitybycycle,meanqualitybycyclepdf,qualityscoredistribution,qualityscoredistributionpdf,hsmetrics,bamindexstats -#LOGS log -#EXES alignmentmetricsjar,gcbiasmetricsjar,insertsizemetricsjar,meanqualitybycyclejar,qualityscoredistributionjar,hsmetricsjar,bamindexstatsjar -#TARGETS - -java -jar -Xmx4g ${alignmentmetricsjar} \ -I=${sortedbam} \ -O=${alignmentmetrics} \ -R=${indexfile} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar ${gcbiasmetricsjar} \ -R=${indexfile} \ -I=${sortedbam} \ -O=${gcbiasmetrics} \ -CHART=${gcbiasmetricspdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar ${insertsizemetricsjar} \ -I=${sortedbam} \ -O=${insertsizemetrics} \ -H=${insertsizemetricspdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -# Overwrite the PDFs that were just created by nicer onces: -${recreateinsertsizepdfR} \ ---insertSizeMetrics ${insertsizemetrics} \ ---pdf ${insertsizemetricspdf} - -java -jar ${meanqualitybycyclejar} \ -I=${sortedbam} \ -O=${meanqualitybycycle} \ -CHART=${meanqualitybycyclepdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -java -jar ${qualityscoredistributionjar} \ -I=${sortedbam} \ -O=${qualityscoredistribution} \ -CHART=${qualityscoredistributionpdf} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} - -<#if capturingKit != "None"> - java -jar -Xmx4g ${hsmetricsjar} \ - INPUT=${sortedbam} \ - OUTPUT=${hsmetrics} \ - BAIT_INTERVALS=${baitintervals} \ - TARGET_INTERVALS=${targetintervals} \ - VALIDATION_STRINGENCY=LENIENT \ - TMP_DIR=${tempdir} -<#else> - echo "## net.sf.picard.metrics.StringHeader" > ${hsmetrics} - echo "#" >> ${hsmetrics} - echo "## net.sf.picard.metrics.StringHeader" >> ${hsmetrics} - echo "#" >> ${hsmetrics} - echo "" >> ${hsmetrics} - echo "## METRICS CLASS net.sf.picard.analysis.directed.HsMetrics" >> ${hsmetrics} - echo "BAIT_SETCS CLASSGENOME_SIZE.sf.pBAIT_TERRITORY.dTARGET_TERRITORYs BAIT_DESIGN_EFFICIENCY TOTAL_READS PF_READS PF_UNIQUE_READS PCT_PF_READS PCT_PF_UQ_READS PF_UQ_READS_ALIGNED PCT_PF_UQ_READS_ALIGNED PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES ON_TARGET_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT ZERO_CVG_TARGETS_PCT FOLD_80_BASE_PENALTY PCT_TARGET_BASES_2X PCT_TARGET_BASES_10X PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X HS_LIBRARY_SIZE HS_PENALTY_1None NA_PENALNA_20X NA_PENALNA_30X NA_DROPONA NA_DROPONA NAMPLE NABRARY NAAD_GRONA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA" >> ${hsmetrics} - - -java -jar ${bamindexstatsjar} \ -INPUT=${sortedbam} \ -VALIDATION_STRINGENCY=LENIENT \ -TMP_DIR=${tempdir} \ -> ${bamindexstats} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/PicardQCrecal.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/PicardQCrecal.ftl deleted file mode 100644 index 16f296e8fc..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/PicardQCrecal.ftl +++ /dev/null @@ -1,24 +0,0 @@ -#MOLGENIS walltime=20:00:00 mem=5 - -#FOREACH externalSampleID -<#assign runtimelog = runtimelog[0] /> -<#assign fileprefix = "externalSampleID " + externalSampleID> - -###### Renaming because we call another protocol: -#inputs: -<#assign sortedbam=mergedbam /> - -#outputs: -<#assign alignmentmetrics=samplealignmentmetrics /> -<#assign gcbiasmetrics=samplegcbiasmetrics /> -<#assign gcbiasmetricspdf=samplegcbiasmetricspdf /> -<#assign insertsizemetrics=sampleinsertsizemetrics /> -<#assign insertsizemetricspdf=sampleinsertsizemetricspdf /> -<#assign meanqualitybycycle=samplemeanqualitybycycle /> -<#assign meanqualitybycyclepdf=samplemeanqualitybycyclepdf /> -<#assign qualityscoredistribution=samplequalityscoredistribution /> -<#assign qualityscoredistributionpdf=samplequalityscoredistributionpdf /> -<#assign hsmetrics=samplehsmetrics /> -<#assign bamindexstats=samplebamindexstats /> - -<#include "PicardQC.ftl"> \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/QCReport.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/QCReport.ftl deleted file mode 100644 index ae20fdc1bd..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/QCReport.ftl +++ /dev/null @@ -1,88 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:05:00 -#FOREACH project -#DOCUMENTATION Documentation of QCReport.ftl, ${getStatisticsScript} - -<#include "Helpers.ftl"/> - -# We need some parameters folded per sample: -<#assign folded = foldParameters(parameters,"project,externalSampleID") /> -<#assign samplehsmetrics = stringList(folded, "samplehsmetrics") /> -<#assign samplealignmentmetrics = stringList(folded, "samplealignmentmetrics") /> -<#assign sampleinsertsizemetrics = stringList(folded, "sampleinsertsizemetrics") /> -<#assign sampleconcordancefile = stringList(folded, "sampleconcordancefile") /> -<#assign externalSampleIDfolded = stringList(folded, "externalSampleID") /> -<#assign snpsfinalvcftabletypefolded = stringList(folded, "snpsfinalvcftabletype") /> -<#assign snpsfinalvcftableclassfolded = stringList(folded, "snpsfinalvcftableclass") /> -<#assign snpsfinalvcftableimpactfolded = stringList(folded, "snpsfinalvcftableimpact") /> -<#--assign typetableoutfolded = stringList(folded, "typetableout") /> -<#assign classtableoutfolded = stringList(folded, "classtableout") /> -<#assign impacttableoutfolded = stringList(folded, "impacttableout") /--> - -# parameters in *.tex template: -<#assign samplecoverageplotpdf = stringList(folded, "samplecoverageplotpdf") /> -<#assign sampleinsertsizemetricspdf = stringList(folded, "sampleinsertsizemetricspdf") /> -<#assign samplegcbiasmetricspdf = stringList(folded, "samplegcbiasmetricspdf") /> - -inputs ${ssvQuoted(samplehsmetrics)} -inputs ${ssvQuoted(samplealignmentmetrics)} -inputs ${ssvQuoted(sampleinsertsizemetrics)} -inputs ${ssvQuoted(dedupmetrics)} -inputs ${ssvQuoted(sampleconcordancefile)} -inputs ${qcstatisticscolnames} - -export PATH=${R_HOME}/bin:<#noparse>${PATH} -export R_LIBS=${R_LIBS} - -# get general sample statistics -Rscript ${getStatisticsScript} \ ---hsmetrics ${csvQuoted(samplehsmetrics)} \ ---alignment ${csvQuoted(samplealignmentmetrics)} \ ---insertmetrics ${csvQuoted(sampleinsertsizemetrics)} \ ---dedupmetrics ${csvQuoted(dedupmetrics)} \ ---concordance ${csvQuoted(sampleconcordancefile)} \ ---sample ${csvQuoted(externalSampleIDfolded)} \ ---colnames ${qcstatisticscolnames} \ ---csvout ${qcstatisticscsv} \ ---tableout ${qcstatisticstex} \ ---descriptionout ${qcstatisticsdescription} \ ---baitsetout ${qcbaitset} \ ---qcdedupmetricsout ${qcdedupmetricsout} - -# get dedup info per flowcell-lane-barcode/sample -Rscript ${getDedupInfoScript} \ ---dedupmetrics ${csvQuoted(dedupmetrics)} \ ---flowcell ${csvQuoted(flowcell)} \ ---lane ${csvQuoted(lane)} \ ---sample ${csvQuoted(externalSampleID)} \ ---paired TRUE \ ---qcdedupmetricsout "${qcdedupmetricsout}" - -# get snp stats per sample -Rscript ${createsnptablescript} \ ---sample ${csvQuoted(externalSampleIDfolded)} \ ---type ${csvQuoted(snpsfinalvcftabletypefolded)} \ ---class ${csvQuoted(snpsfinalvcftableclassfolded)} \ ---impact ${csvQuoted(snpsfinalvcftableimpactfolded)} \ ---typetableout "${typetableout}" \ ---classtableout "${classtableout}" \ ---impacttableout "${impacttableout}" - - -# create workflow figure -echo "${graph(workflowElements)}" | ${dot} -Tpng > ${workflowpng} - -# save latex template in file -echo "<#include "QCReportTemplate.tex"/>" > ${qcstatisticstexreport} - -pdflatex -output-directory=${qcdir} ${qcstatisticstexreport} -pdflatex -output-directory=${qcdir} ${qcstatisticstexreport} <#--do twice to fill all cross references--> diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/QCReportTemplate.tex b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/QCReportTemplate.tex deleted file mode 100644 index ce3306d522..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/QCReportTemplate.tex +++ /dev/null @@ -1,162 +0,0 @@ -\documentclass[a4paper,12pt]{article} -\usepackage{nameref} -\usepackage{grffile} -\usepackage{graphicx} -\usepackage[strings]{underscore} -\usepackage{verbatim} -\usepackage{wrapfig} -\usepackage{lastpage} - -\begin{comment} -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# -\end{comment} - -\newenvironment{narrow}[2]{ - \begin{list}{}{ - \setlength{\leftmargin}{#1} - \setlength{\rightmargin}{#2} - \setlength{\listparindent}{\parindent} - \setlength{\itemindent}{\parindent} - \setlength{\parsep}{\parskip} - } - \item[] -}{\end{list}} - -\title{Next Generation Sequencing report} -\author{\small Genome Analysis Facility (GAF), Genomics Coordination Centre (GCC)\\\\ -\small University Medical Centre Groningen} - -\begin{document} -\maketitle -\thispagestyle{empty} -\vspace{40mm} - -\begin{table}[h] - \centering - \begin{tabular}{l l} - \hline - \multicolumn{2}{l}{\textbf{Report}} \\\\ - Created on & \today \\\\ - Number of pages & \\pageref{LastPage} \\\\ \\\\ - Generated by & MOLGENIS Compute \\\\ - \\\\ - \multicolumn{2}{l}{\textbf{Project}} \\\\ - Project name & ${project} \\\\ - Number of samples & ${samplecoverageplotpdf?size} \\\\ - \\\\ - \multicolumn{2}{l}{\textbf{Customer}} \\\\ - Principal investigator & ${contact?replace("<", "/ ")?replace(">", "")} \\\\ - \\\\ - \multicolumn{2}{l}{\textbf{Contact}} \\\\ - Name & Cleo C. van Diemen \\\\ - E-mail & c.c.van.diemen@umcg.nl \\\\ - \hline - \end{tabular} -\end{table} - -\clearpage -\tableofcontents - -\clearpage -\section*{Introduction} -\addcontentsline{toc}{section}{Introduction} -This report describes a series of statistics about your sequencing data. Together with this report you'll receive a SNP-list. If you, in addition, also want the raw data, then please notify us via e-mail. In any case we'll delete the raw data, three months after \today. - -\clearpage -\section*{Project analysis results} -\addcontentsline{toc}{section}{Project analysis results} - -\subsection*{Overview statistics} -\addcontentsline{toc}{subsection}{Overview statistics} -\label{subsect:overviewstatistics} -% statistics table -\input{${qcstatisticstex}} - -\begin{minipage}{\textwidth} - Name of the bait set(s) used in the hybrid selection for this project:\\\\ - \textbf{\input{${qcbaitset}}} -\end{minipage} - -\clearpage -\subsection*{Description statistics table} -\addcontentsline{toc}{subsection}{Description statistics table} -\begin{table}[h!] - \centering - \begin{tabular}{r p{12cm}} - \input{${qcstatisticsdescription}} - \end{tabular} -\end{table} - -\clearpage -\subsection*{Capturing} -\addcontentsline{toc}{subsection}{Capturing} -The following figures show the cumulative depth distribution in the target regions that are located on \emph{chromosome 1}. The fractions of bases that is covered with at least 10x, 20x and 30x are marked with a dot. Please see section \"\\nameref{subsect:overviewstatistics}\" for the full coverage statistics per sample; \emph{i.e.}, in the target regions on \emph{all chromosomes}. -${figures(samplecoverageplotpdf)} - -\clearpage -\subsection*{Insert size distribution} -\addcontentsline{toc}{subsection}{Insert size distribution} -The following figures show the insert size distribution per sample. Insert refers to the base pairs that are ligated between the adapters. -${figures(sampleinsertsizemetricspdf)} - -%\clearpage -%\subsection*{Demultiplex statistics} -%\addcontentsline{toc}{subsection}{Demultiplex statistics} -%Under construction... -%displaystats(demultiplexstats) - -%\clearpage -%\subsection*{GC metrics} -%\addcontentsline{toc}{subsection}{GC metrics} -%The following figures show the GC-content distribution per sample. -%${figures(samplegcbiasmetricspdf)} - -%\clearpage -%\subsection*{SNP statistics} -%\addcontentsline{toc}{subsection}{SNP statistics} -%The tables with caption 'Functional type', 'Functional class' and 'Functional impact', classify the SNPs, based on Ensembl, build 37.64. -%\input{${typetableout}} -%\input{${classtableout}} -%\input{${impacttableout}} - -\clearpage -\subsection*{Duplication rates} -\addcontentsline{toc}{subsection}{Duplication rates} -\input{${qcdedupmetricsout}} - -\clearpage -\section*{Appendix 1: Genome Analysis Facility Pipeline} -\addcontentsline{toc}{section}{Appendix 1: Genome Analysis Facility Pipeline} -\subsection*{Exome sequencing} -\addcontentsline{toc}{subsection}{Exome sequencing} -\begin{wrapfigure}{r}{0.5\textwidth} - \begin{center} - \includegraphics[width=.5\textwidth]{${gaffig}} - \end{center} - \caption{Workflow in the lab} - \label{fig:wet} -\end{wrapfigure} -Figure \ref{fig:wet} illustrated the basic experimental process of exome capture sequencing. The Genomic DNA sample was randomly fragmented using Nebulisation. Then barcoded adapters were ligated to both ends of the resulting fragments, according the standard New England Biolabs protocol. Fragments with an insert size of 220 bp on average were excised using the Caliper XT gel system and the extracted DNA was amplified with PCR. - -The quality of the product was verified on the BioRad Experion instrument. If the quality of the product meets the criteria, the product is multiplexed in an equimolar pool of 4 simular products. This pool is hybridized to the Agilent SureSelect All exon V2, according the provided protocol. After amplification of the enriched products with PCR the quality of the products is verified on the BioRad Experion instrument and Paired End sequenced on the HiSeq2000 with 100 bp reads. Image Files were processed using standard Illumina basecalling software and the generated reads are ready for downstream processing after demultiplexing. - -\clearpage -\section*{Appendix 2: Bioinformatics pipeline} -\addcontentsline{toc}{section}{Appendix 2: Bioinformatics pipeline} -Your samples have been anlayzed with bioinformatics pipeline shown in Figure \ref{fig:dry}. -\begin{figure}[h] - \caption{Bioinformatics pipeline. The ovals describe the steps in the pipeline. The arrows indicate the work flow of data between the steps.} - \begin{center} - \includegraphics[width=.9\textwidth]{${workflowpng}} - \end{center} - \label{fig:dry} -\end{figure} -\end{document} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Realign.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Realign.ftl deleted file mode 100644 index c3f28c606b..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Realign.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=10 cores=1 - - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -inputs "${realignTargets}" -alloutputsexist "${realignedbam}" - -java -Djava.io.tmpdir=${tempdir} -Xmx10g -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T IndelRealigner \ --U ALLOW_UNINDEXED_BAM \ --I ${dedupbam} \ ---out ${realignedbam} \ --targetIntervals ${realignTargets} \ --R ${indexfile} \ --D ${dbsnprod} \ --B:indels,VCF ${pilot1KgVcf} \ --knownsOnly \ --LOD 0.4 \ --maxReads 2000000 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/RealignTargetCreator.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/RealignTargetCreator.ftl deleted file mode 100644 index f9e3dd409f..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/RealignTargetCreator.ftl +++ /dev/null @@ -1,29 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=10 - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -alloutputsexist \ - "${realignTargets}" - -java -Xmx10g -jar -Djava.io.tmpdir=${tempdir} \ -${genomeAnalysisTKjar} \ --l INFO \ --T RealignerTargetCreator \ --U ALLOW_UNINDEXED_BAM \ --I ${dedupbam} \ --R ${indexfile} \ --D ${dbsnprod} \ --B:indels,VCF ${pilot1KgVcf} \ --o ${realignTargets} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Recalibrate.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Recalibrate.ftl deleted file mode 100644 index d9a474fcd5..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Recalibrate.ftl +++ /dev/null @@ -1,26 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:59:00 mem=4 cores=1 - -inputs "${indexfile}" -inputs "${matefixedbam}" -inputs "${matefixedcovariatecsv}" -alloutputsexist "${recalbam}" - -java -jar -Xmx4g \ -${genomeAnalysisTKjar} \ --l INFO \ --T TableRecalibration \ --U ALLOW_UNINDEXED_BAM \ --R ${indexfile} \ --I ${matefixedbam} \ ---recal_file ${matefixedcovariatecsv} \ ---out ${recalbam} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/RunGerald.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/RunGerald.ftl deleted file mode 100644 index 6e4d1f5a91..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/RunGerald.ftl +++ /dev/null @@ -1,20 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:59:00 mem=12 cores=8 -#FOREACH run - -#Source GAF bash -. ${gafhome}/gaf.bashrc - - -perl ${gafscripts}/run_GERALD.pl \ --run ${run} \ --samplecsv ${McWorksheet} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamSort.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamSort.ftl deleted file mode 100644 index f18946a9ee..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamSort.ftl +++ /dev/null @@ -1,37 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 - -#INPUTS bamfile -#OUTPUTS sortedbam,sortedbamindex -#LOGS log -#EXES sortsamjar,buildbamindexjar -#TARGETS - -inputs "${bamfile}" -alloutputsexist \ - "${sortedbam}" \ - "${sortedbamindex}" - -java -jar -Xmx3g ${sortsamjar} \ -INPUT=${bamfile} \ -OUTPUT=${sortedbam} \ -SORT_ORDER=coordinate \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} - -java -jar -Xmx3g ${buildbamindexjar} \ -INPUT=${sortedbam} \ -OUTPUT=${sortedbamindex} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=1000000 \ -TMP_DIR=${tempdir} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamSortRecal.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamSortRecal.ftl deleted file mode 100644 index 6662ebb180..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamSortRecal.ftl +++ /dev/null @@ -1,7 +0,0 @@ -#MOLGENIS walltime=35:59:00 mem=4 - -<#assign bamfile=recalbam /> -<#assign sortedbam=sortedrecalbam /> -<#assign sortedbamindex=sortedrecalbamindex /> - -<#include "SamSort.ftl" /> \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamToBam.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamToBam.ftl deleted file mode 100644 index 50960e484f..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/SamToBam.ftl +++ /dev/null @@ -1,27 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=3 - -#INPUTS samfile -#OUTPUTS bamfile -#LOGS log -#EXES samtobamjar -#TARGETS - -inputs "${samfile}" -alloutputsexist "${bamfile}" - -java -jar -Xmx3g ${samtobamjar} \ -INPUT=${samfile} \ -OUTPUT=${bamfile} \ -VALIDATION_STRINGENCY=LENIENT \ -MAX_RECORDS_IN_RAM=2000000 \ -TMP_DIR=${tempdir} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/UnifiedGenotyper.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/UnifiedGenotyper.ftl deleted file mode 100644 index 1d18d834e8..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/UnifiedGenotyper.ftl +++ /dev/null @@ -1,32 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=46:00:00 mem=8 cores=5 -#FOREACH externalSampleID - -inputs "${mergedbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -alloutputsexist \ - "${snpsvcf}" \ - "${snpsvcf}.metrics" - -java -Xmx8g -Djava.io.tmpdir=${tempdir} -XX:+UseParallelGC -XX:ParallelGCThreads=1 -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T UnifiedGenotyper \ --I ${mergedbam} \ ---out ${sample}.snps.vcf \ --R ${indexfile} \ --D ${dbsnprod} \ --stand_call_conf 30.0 \ --stand_emit_conf 10.0 \ --nt 4 \ ---metrics_file ${sample}.snps.vcf.metrics \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VQSRApplyRecal.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VQSRApplyRecal.ftl deleted file mode 100644 index 2ae94dac00..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VQSRApplyRecal.ftl +++ /dev/null @@ -1,34 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/Realign.ftl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: pneerincx $ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=10 cores=1 - - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -inputs "${realignTargets}" -alloutputsexist "${realignedbam}" - -java -Djava.io.tmpdir=${tempdir} -Xmx10g -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T IndelRealigner \ --U ALLOW_UNINDEXED_BAM \ --I ${dedupbam} \ ---out ${realignedbam} \ --targetIntervals ${realignTargets} \ --R ${indexfile} \ --D ${dbsnprod} \ --B:indels,VCF ${pilot1KgVcf} \ --knownsOnly \ --LOD 0.4 \ --maxReads 2000000 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VQSRVariantRecal.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VQSRVariantRecal.ftl deleted file mode 100644 index 2072c4713e..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VQSRVariantRecal.ftl +++ /dev/null @@ -1,33 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL: http://www.molgenis.org/svn/molgenis_apps/trunk/modules/compute/protocols/Realign.ftl $ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy: pneerincx $ -# ===================================================== -# - -#MOLGENIS walltime=35:59:00 mem=4 cores=1 - -inputs "${dedupbam}" -inputs "${indexfile}" -inputs "${dbsnprod}" -inputs "${pilot1KgVcf}" -inputs "${realignTargets}" -alloutputsexist "${realignedbam}" - -java -Djava.io.tmpdir=${tempdir} -Xmx4g -jar \ -${genomeAnalysisTKjar} \ --l INFO \ --T VariantRecalibrator \ --R ${indexfile} \ - -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \ - -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ - -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \ - -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_132.b37.vcf \ --B:concordantSet,VCF,known=true,training=true,truth=true,prior=10.0 path/to/concordantSet.vcf - -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ \ - -recalFile path/to/output.recal \ - -tranchesFile path/to/output.tranches \ - -rscriptFile path/to/output.plots.R diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VariantAnnotator.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VariantAnnotator.ftl deleted file mode 100644 index 4d0abeaadf..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VariantAnnotator.ftl +++ /dev/null @@ -1,48 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:00:00 mem=10 -#FOREACH externalSampleID - -inputs "${snpeffjar}" -inputs "${snpeffconfig}" -inputs "${snpsgenomicannotatedvcf}" -inputs "${mergedbam}" -inputs "${dbsnpvcf}" -inputs "${indexfile}" -<#if capturingKit != "None">inputs "${baitsbed}" -alloutputsexist "${snpeffsummaryhtml}" "${snpeffintermediate}" "${snpsfinalvcf}" - -####Create snpEFF annotations on original input file#### -java -Xmx4g -jar ${snpeffjar} \ -eff \ --v \ --c ${snpeffconfig} \ --i vcf \ --o vcf \ -GRCh37.64 \ --onlyCoding true \ --stats ${snpeffsummaryhtml} \ -${snpsgenomicannotatedvcf} \ -> ${snpeffintermediate} - -####Annotate SNPs with snpEff information#### -java -jar -Xmx4g ${genomeAnalysisTKjar1411} \ --T VariantAnnotator \ ---useAllAnnotations \ ---excludeAnnotation MVLikelihoodRatio \ ---excludeAnnotation TechnologyComposition \ --I ${mergedbam} \ ---snpEffFile ${snpeffintermediate} \ --D ${dbsnpvcf} \ --R ${indexfile} \ ---variant ${snpsgenomicannotatedvcf} \<#if capturingKit != "None"> --L ${baitsbed} \ --o ${snpsfinalvcf} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VariantFiltration.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VariantFiltration.ftl deleted file mode 100644 index f495685fbe..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VariantFiltration.ftl +++ /dev/null @@ -1,58 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=45:00:00 mem=10 -inputs "${snpsgenomicannotatedvcf}" -inputs "${indelsmaskbed}" -inputs "${indexfile}" -<#if capturingKit != "None">inputs "${baitintervals}" -inputs "${dbsnprod}" -alloutputsexist "${snpsgenomicannotatedfilteredvcf}" - -rm ${snpsgenomicannotatedvcf}.idx - -## -# http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v2 -## -# HARD_TO_VALIDATE: more than 10% (or more than 3) of the reads have mapping quality 0 -# MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1) -## -# "Note that For exomes, a straight DP filter shouldn't be used because the -# relationship between misalignments and depth isn't clear for capture data. -# Note that as of Dec. 2010 we no longer recommend using AB to filter, as (1) -# it's not generated by the UG by default any more and (2) QD is a better, -# and largely equivalent, filter." -# QUAL < 30.0 || QD < 5.0 || HRun > 5 || SB > -0.10 -# The UG itself: the confidence score and emission thresholds (-stand_call_conf -# and -stand_emit_conf, both Phredscores) are chosen based on the (expected) -# overall coverage. Anything below the emission threshold is not called, -# anything between the two thresholds is flagged LowQual. -# To discuss: a straight DP filter, set to 5 or 10? Or higher? Why, why not? -# For now, I'll include an expression to mark SNPs with a depth of 10 or higher -# with "DEPTH_10". -## - -java -jar -Xmx10g ${genomeAnalysisTKjar} \ --l INFO \ --T VariantFiltration \ --B:variant,VCF ${snpsgenomicannotatedvcf} \ --B:mask,Bed ${indelsmaskbed} \ --R ${indexfile} \<#if capturingKit != "None"> --L ${baitintervals} \ --D ${dbsnprod} \ --o ${snpsgenomicannotatedfilteredvcf} \ ---maskName InDel \ ---clusterWindowSize 10 \ ---filterExpression "QUAL < 30.0 || QD < 5.0 || HRun > 5 || SB > -0.10" \ ---filterName GATK_EXOME_standard \ ---filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \ ---filterName "HARD_TO_VALIDATE" \ ---filterExpression "DP > 10" \ ---filterName "DEPTH_10" \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VcfToTable.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VcfToTable.ftl deleted file mode 100644 index 289c6fa893..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/VcfToTable.ftl +++ /dev/null @@ -1,43 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:40:00 -#FOREACH externalSampleID - -inputs "${snpsfinalvcf}" -alloutputsexist "${snpsfinalvcftable}" "${snpsfinalvcftabletype}" "${snpsfinalvcftableclass}" "${snpsfinalvcftableimpact}" - -####Transform VCF file into tabular file#### -python ${vcf2tablepy} \ -${snpsfinalvcf} \ --f CHROM,POS,ID,REF,ALT,QUAL,FILTER,AB,AC,AF,ALTFWD,ALTREV,AN,\ -BaseCounts,BaseQRankSum,DB,DP,DS,Dels,FS,GC,HRun,HW,HaplotypeScore,\ -LowMQ,MQ,MQ0,MQ0Fraction,MQRankSum,PercentNBaseSolid,QD,ReadPosRankSum,REFFWD,REFREV,SB,SBD,\ -SNPEFF_AMINO_ACID_CHANGE,SNPEFF_CODON_CHANGE,SNPEFF_EFFECT,SNPEFF_EXON_ID,SNPEFF_FUNCTIONAL_CLASS,\ -SNPEFF_GENE_BIOTYPE,SNPEFF_GENE_NAME,SNPEFF_IMPACT,SNPEFF_TRANSCRIPT_ID,Samples,TDT,\ -dbSNP132.AF,dbSNP132.ASP,dbSNP132.ASS,dbSNP132.CDA,dbSNP132.CFL,dbSNP132.CLN,dbSNP132.DSS,dbSNP132.G5,\ -dbSNP132.G5A,dbSNP132.GCF,dbSNP132.GMAF,dbSNP132.GNO,dbSNP132.HD,dbSNP132.INT,dbSNP132.KGPROD,dbSNP132.KGPilot1,dbSNP132.KGPilot123,\ -dbSNP132.KGVAL,dbSNP132.LSD,dbSNP132.MTP,dbSNP132.MUT,dbSNP132.NOC,dbSNP132.NOV,dbSNP132.NS,dbSNP132.NSF,dbSNP132.NSM,dbSNP132.OM,\ -dbSNP132.OTH,dbSNP132.PH1,dbSNP132.PH2,dbSNP132.PH3,dbSNP132.PM,dbSNP132.PMC,dbSNP132.R3,dbSNP132.R5,dbSNP132.REF,dbSNP132.RSPOS,\ -dbSNP132.RV,dbSNP132.S3D,dbSNP132.SAO,dbSNP132.SCS,dbSNP132.SLO,dbSNP132.SSR,dbSNP132.SYN,dbSNP132.TPA,dbSNP132.U3,dbSNP132.U5,dbSNP132.VC,\ -dbSNP132.VLD,dbSNP132.VP,dbSNP132.WGT,dbSNP132.WTD,dbSNP132.dbSNPBuildID,\ -sumGLbyD,\ -FORMAT,${externalSampleID} \ --o ${snpsfinalvcftable} - -# get SNP statistics -perl ${snpannotationstatspl} \ --vcf_table ${snpsfinalvcftable} \ --typefile ${snpsfinalvcftabletype} \ --classfile ${snpsfinalvcftableclass} \ --impactfile ${snpsfinalvcftableimpact} \ --snptypes DOWNSTREAM,INTERGENIC,INTRAGENIC,INTRON,NON_SYNONYMOUS_CODING,NON_SYNONYMOUS_START,SPLICE_SITE_ACCEPTOR,SPLICE_SITE_DONOR,START_GAINED,START_LOST,STOP_GAINED,STOP_LOST,SYNONYMOUS_CODING,SYNONYMOUS_STOP,UPSTREAM,UTR_3_PRIME,UTR_5_PRIME \ --snpclasses MISSENSE,NONSENSE,NONE,SILENT \ --snpimpacts HIGH,LOW,MODERATE,MODIFIER \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Zipfq.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Zipfq.ftl deleted file mode 100644 index f925242287..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/Zipfq.ftl +++ /dev/null @@ -1,28 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=10:00:00 nodes=1 cores=1 mem=10 - -<#if seqType == "SR"> - # assume single read - alloutputsexist ${leftbarcodefqgz} - inputs ${leftbarcodefq} -<#else> - # assume paired end - alloutputsexist ${leftbarcodefqgz} ${rightbarcodefqgz} - inputs ${leftbarcodefq} ${rightbarcodefq} - - -# The following code gzips files and removes original file -# However, in the case of a symlink, the symlink is removed. - gzip -f ${leftbarcodefq} -<#if seqType == "PE"> - gzip -f ${rightbarcodefq} - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/getdata.sh b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/getdata.sh deleted file mode 100644 index 03d178d362..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/getdata.sh +++ /dev/null @@ -1,102 +0,0 @@ -#!/bin/bash - -getdata() -{ -CLUSTER="cluster"; -GRID="grid"; - -INPUT="input"; -OUTPUT="output"; -EXE="exe"; - -ARGS=($@) -BACKEND="${ARGS[0]}"; -OPERATION="${ARGS[1]}"; - -NUMBER="${#ARGS[@]}"; -MIN=4 - -if [ "$NUMBER" -gt "$MIN" ] -then - - for (( i=4; i<$#; i++ )) - do - value="${ARGS[2]}${ARGS[3]}${ARGS[$i]}"; - - if [ "$BACKEND" == "$CLUSTER" ] - then - #check if data exists on the cluster - if test ! -e $value; - then - echo "$value is missing" 1>&2 - fi - fi - - if [ "$BACKEND" == "$GRID" ] - then - #download/upload data on the grid - if [ "$OPERATION" == "$INPUT" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]}${ARGS[$i]} - fi - - if [ "$OPERATION" == "$OUTPUT" ] - then - lcg-cr -l lfn://grid$value file:///$TMPDIR/${INPUTS[2]}${INPUTS[$i]} - fi - - #download executable - if [ "$OPERATION" == "$EXE" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]}${ARGS[$i]} - chmod 755 $TMPDIR${ARGS[3]}${ARGS[$i]} - fi - - #check sum on the execution node - echo -n "SUM_ADLER32_${ARGS[3]}${ARGS[$i]} " - adler32 file:///$TMPDIR${ARGS[3]}${ARGS[$i]} - fi - - done - -else - - if [ "$BACKEND" == "$CLUSTER" ] - then - #check if data exists on the cluster - if test ! -e $value; - then - echo "$value is missing" 1>&2 - fi - fi - - if [ "$BACKEND" == "$GRID" ] - then - #download/upload data on the grid - if [ "$OPERATION" == "$INPUT" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]} - fi - - if [ "$OPERATION" == "$OUTPUT" ] - then - lcg-cr -l lfn://grid$value file:///$TMPDIR/${INPUTS[2]} - fi - - #download executable - if [ "$OPERATION" == "$EXE" ] - then - lcg-cp lfn://grid$value file:///$TMPDIR${ARGS[3]} - chmod 755 $TMPDIR${ARGS[3]} - fi - - #check sum on the execution node - echo -n "SUM_ADLER32_${ARGS[3]}${ARGS[$i]} " - adler32 file:///$TMPDIR${ARGS[3]} - fi - -fi - -} - - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/gwas/FixColumns.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/gwas/FixColumns.ftl deleted file mode 100644 index 4d50601658..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/gwas/FixColumns.ftl +++ /dev/null @@ -1,53 +0,0 @@ -# -# ===================================================== -# $Id$ -# $URL$ -# $LastChangedDate$ -# $LastChangedRevision$ -# $LastChangedBy$ -# ===================================================== -# - -#MOLGENIS walltime=00:10:00 -#FOREACH project - -# -# Change permissions. -# -umask 0007 - -# -# Create project dirs. -# -mkdir -p ${projectRawDataDir} -mkdir -p ${projectJobsDir} -mkdir -p ${projectLogsDir} -mkdir -p ${projectIntermediateDir} -mkdir -p ${projectResultsDir} - -<#if familyIDs?exists> - ${plink} --noweb --silent \ - --bfile ${plinkFileRaw} \ - --update-ids ${familyIDs} \ - --make-bed --out ${plinkFileFixedFamilies} -<#else> - ln -s ${plinkFileRaw} ${plinkFileFixedFamilies} - - -<#if parentIDs?exists> - ${plink} --noweb --silent \ - --bfile ${plinkFileFixedFamilies} \ - --update-parents ${parentIDs} \ - --make-bed --out ${plinkFileFixedParents} -<#else> - ln -s ${plinkFileFixedFamilies} ${plinkFileFixedParents} - - -<#if removeIDs?exists> - ${plink} --noweb --silent \ - --bfile ${plinkFileFixedParents} \ - --remove ${removeIDs} \ - --make-bed --out ${plinkFileClean} -<#else> - ln -s ${plinkFileFixedParents} ${plinkFileClean} - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/CustomSubmit.sh.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/CustomSubmit.sh.ftl deleted file mode 100644 index e7eb4ee93a..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/CustomSubmit.sh.ftl +++ /dev/null @@ -1,9 +0,0 @@ -DIR="$( cd "$( dirname "<#noparse>${BASH_SOURCE[0]}" )" && pwd )" -touch $DIR/${workflowfilename}.started - -<#foreach j in jobs> -#${j.name} -${j.name}=$(qsub -N ${j.name}<#if j.prevSteps_Name?size > 0> -W depend=afterok<#foreach d in j.prevSteps_Name>:$${d} ${j.name}.sh) -echo $${j.name} -sleep 8 - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Footer.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Footer.ftl deleted file mode 100644 index 19c8a45f39..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Footer.ftl +++ /dev/null @@ -1,2 +0,0 @@ -<#if defaultInterpreter = "R"><@Rend/> -<@end/> \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Header.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Header.ftl deleted file mode 100644 index 56d943bf8a..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Header.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#if scheduler == "PBS"> -#!/bin/bash -#PBS -N ${jobname} -#PBS -q ${clusterQueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${mem} -#PBS -e ${jobname}.err -#PBS -o ${jobname}.out - -<#elseif scheduler == "SGE"> -#!/bin/bash -#$ -N ${jobname} -#$ -q ${clusterQueue} -#$ -p ${cores} -#$ -l h_rt=${walltime} -#$ -l h_vmem=${mem} -#$ -e ${jobname}.err -#$ -o ${jobname}.out - - - - - -# Configures the GCC bash environment -. ${root}/gcc.bashrc - -<#include "Macros.ftl"/> -<@begin/> - -<#if defaultInterpreter = "R"><@Rbegin/> \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Helpers.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Helpers.ftl deleted file mode 100644 index e3c7d2c267..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Helpers.ftl +++ /dev/null @@ -1,86 +0,0 @@ -<#function csvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function csv items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + ","> - - <#local result = result + "" + item + ""> - - <#return result> - - -<#function ssvQuoted items> - <#local result = ""> - <#list items as item> - <#if item_index != 0> - <#local result = result + " "> - - <#local result = result + "\"" + item + "\""> - - <#return result> - - -<#function figures figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleIDfolded[i]}}}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function figuresInsertSize figs> - <#local result = ""> - <#assign maxnfigs=4 /> - <#assign nplots=figs?size /> - <#list 0..(nplots - 1) as i> - <#if i % maxnfigs = 0><#local result = result + "\\begin{figure}[ht]"> - <#local result = result + "\\begin{minipage}{0.5\\linewidth}"> - <#local result = result + "\\centering"> - <#local result = result + "\\includegraphics[width=\\textwidth]{${figs[i]}}"> - <#local result = result + "\\caption{sample \\textbf{${externalSampleID[i]}}, flowcell \\textbf{${flowcell[i]}}, lane \\textbf{${lane[i]}}}}"> - <#local result = result + "\\end{minipage}"> - <#local result = result + "\\hspace{1cm}"><#if (i+1) = nplots || (i+1) % maxnfigs = 0><#local result = result + "\\end{figure}"> - <#return result> - - -<#function graph workflowElements> - <#local result = "digraph G {"> - <#list workflowElements as el> - <#-- first nodes --> - <#local result = result + el.name + "; "/> - <#-- edges --> - <#list el.previousSteps_Name as other><#local result = result + other + "->" + el.name + ";"/> - - <#local result = result + "}"> - <#return result> - - -<#function unfoldParametersCSV tuple> - <#return freemarkerHelper.unfoldCSV(tuple) /> - - -<#function foldParameters tuple on> - <#return freemarkerHelper.foldOn(tuple, on)/> - - -<#function stringList parameters var> - <#return freemarkerHelper.stringList(parameters, var)/> - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Macros.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Macros.ftl deleted file mode 100644 index 27121e02dd..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/Macros.ftl +++ /dev/null @@ -1,31 +0,0 @@ -<#include "Helpers.ftl"/> -<#macro begin> -##### BEFORE ##### -touch $PBS_O_WORKDIR/${jobname}.out -source ${importscript} -before="$(date +%s)" -echo "Begin job ${jobname} at $(date)" >> $PBS_O_WORKDIR/RUNTIME.log - -echo Running on node: `hostname` - -sleep 60 -###### MAIN ###### - - - -<#macro end > -###### AFTER ###### -after="$(date +%s)" -elapsed_seconds="$(expr $after - $before)" -echo Completed ${jobname} at $(date) in $elapsed_seconds seconds >> $PBS_O_WORKDIR/RUNTIME.log -touch $PBS_O_WORKDIR/${jobname}.finished -######## END ######## - - -<#macro Rbegin> -${R} --vanilla < - -<#macro Rend> -RSCRIPT - \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/beagleOutputToTrityper.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/beagleOutputToTrityper.ftl deleted file mode 100644 index 3a210abc9d..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/beagleOutputToTrityper.ftl +++ /dev/null @@ -1,18 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS imputedoutputbeagle #<-- Add gprobsinput later -#OUTPUTS bgltotrityperoutput -#EXES plink -#TARGETS project,chr - -inputs "${imputedoutputbeagle}" -alloutputsexist "${bgltotrityperoutput}" #<-- Check all beagle outputs, where does the inserted chrnum come from?? - - - -#Convert beagle output to TriTyper format using hacked converter from Harm-Jan (This should be fixed by TriTyper team/developers) -java -jar -Xmx4g ${convertbgltotrityperjar} \ -/target/gpfs2/gcc/home/pdeelen/beagleImputed/imputed.chr20.chr20.bgl.gprobs.gz \ #<-- Change this when known where chrnum is coming from -${bgltotrityperoutput} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/createBglFileFromPlinkData.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/createBglFileFromPlinkData.ftl deleted file mode 100644 index bb20ba1857..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/createBglFileFromPlinkData.ftl +++ /dev/null @@ -1,16 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS plinkdatatransposed -#OUTPUTS beaglefile -#EXES -#TARGETS project,chr - -inputs "${plinkdatatransposed}.tped" -alloutputsexist "${beaglefile}" - -#Create beagle format file to be used for reference (GoNL) beagle phased data -gawk '{$2=$1":"$4; $1="M"; $3=""; $4=""; print $0}' \ -${plinkdatatransposed}.tped \ -> ${beaglefile} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/createMarkerFile.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/createMarkerFile.ftl deleted file mode 100644 index 0c7d4b72b9..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/createMarkerFile.ftl +++ /dev/null @@ -1,46 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS plinkdatatransposed -#OUTPUTS beaglefile -#EXES plink -#TARGETS project,chr - -inputs "${plinkdatatransposed}.tped" -alloutputsexist "${plinkdatatransposed}.frq" -alloutputsexist "${plinkdatatransposed}.log" -alloutputsexist "${plinkdata}.map" -alloutputsexist "${plinkdata}.ped" - - -#Create first part of marker file for beagle -${plink} \ ---tfile ${plinkdatatransposed} \ ---freq \ ---out ${plinkdatatransposed}.frq \ ---noweb - -gawk '$1!="CHR" {print $2,$3,$4}' ${plinkdatatransposed}.frq \ -> ${markerspt1} - - -#Create second part of markers -${plink} \ ---tfile ${plinkdatatransposed} \ ---recode \ ---out ${plinkdata} \ ---noweb - -gawk '{print $2,$4,$1":"$4}' ${plinkdata}.map \ -> ${markerspt2} - - -#Join both markerfiles merging via IDs -join -1 1 -2 1 \ -${markerspt1} \ -${markerspt2} \ -| gawk '{print $5,$4,$2,$3}' \ -> ${markers} #<- define this later when method is finished (include step from perl scripts) - -#####ADD rest of template when steps are exactly known###### \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/imputeWithBeagle.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/imputeWithBeagle.ftl deleted file mode 100644 index cfc6f63b6f..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/imputeWithBeagle.ftl +++ /dev/null @@ -1,23 +0,0 @@ - - -#MOLGENIS walltime=72:00:00 nodes=1 cores=1 mem=35 - -#INPUTS beaglefile,beaglefilephased,markers -#OUTPUTS imputedoutputbeagle.* -#EXES beagle -#TARGETS project,chr - -inputs "${beaglefile}" -inputs "${beaglefilephased}" -inputs "${markers}" -alloutputsexist "${imputedoutputbeagle}" - - -#Impute using Beagle -java -jar -Xmx35g -Djava.io.tmpdir=${tempdir} \ -${beaglejar} \ -unphased=${beaglefile} \ -phased=${beaglefilephased} \ -markers=${markers} \ -missing=0 \ -out=${imputedoutputbeagle} \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/myProject.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/myProject.csv deleted file mode 100644 index dba3761275..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/myProject.csv +++ /dev/null @@ -1,2 +0,0 @@ -project,chr -1240Blood_b37,20 \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/parameters.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/parameters.csv deleted file mode 100644 index 2d2dba6873..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/parameters.csv +++ /dev/null @@ -1,41 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -scheduler,SGE,,, -defaultInterpreter,#!/bin/bash,,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -tooldir,${root}/tools,root dir for tools,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -workflowFile,${McDir}/protocols/imputation/workflowBeagle.csv,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -plink,${tooldir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -homedir,${root}/home/fvandijk,,, -projectdir,${homedir}/${project},,, -plinkdata,${projectdir}/${chr},,, -plinkdatatransposed,${plinkdata}.transposed,,, -beaglefile,${plinkdata}.bgl,,, -beaglefilephased,,Comes from samplesheet,, -markerspt1,${plinkdata}.markers1.txt,,, -markerspt2,${plinkdata}.markers2.txt,,, -markers,${plinkdata}.markers.txt,,, -imputedoutputbeagle,${plinkdata}.imputed,,, -beaglejar,${tooldir}/beagle_3.3_26Dec10/beagle.jar,,, -convertbgltotrityperjar,${tooldir}/dist/BeagleSingleFileConvertToTriTyper.jar,,, -bgltotrityperoutput,${projectdir}/TriTyperOutput/,The trailing backslash is obligatory!,, diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/transposePlinkData.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/transposePlinkData.ftl deleted file mode 100644 index 1ca233bec4..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/transposePlinkData.ftl +++ /dev/null @@ -1,27 +0,0 @@ - - -#MOLGENIS walltime=24:00:00 nodes=1 cores=1 mem=4 - -#INPUTS plinkdata -#OUTPUTS plinkdatatransposed -#EXES plink -#TARGETS project,chr - -inputs "${plinkdata}.bed" -inputs "${plinkdata}.bim" -inputs "${plinkdata}.fam" -inputs "${plinkdata}.map" -inputs "${plinkdata}.ped" -alloutputsexist "${plinkdatatransposed}.tfam" -alloutputsexist "${plinkdatatransposed}.tped" - -#Build in iteration over chromosome! - -#Transpose plink data -${plink} \ ---bfile ${plinkdata} \ ---chr ${chr} \ ---transpose \ ---recode \ ---out ${plinkdatatransposed} \ ---noweb \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/workflowBeagle.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/workflowBeagle.csv deleted file mode 100644 index 9414cfa292..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/protocols/imputation/workflowBeagle.csv +++ /dev/null @@ -1,6 +0,0 @@ -name,protocol_name,PreviousSteps_name -transposePlinkData,transposePlinkData, -createBglFileFromPlinkData,createBglFileFromPlinkData,transposePlinkData -createMarkerFile,createMarkerFile,createBglFileFromPlinkData -imputeWithBeagle,imputeWithBeagle,createMarkerFile -beagleOutputToTrityper,beagleOutputToTrityper,imputeWithBeagle diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-cluster.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-cluster.ftl deleted file mode 100644 index 1308393ee2..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-cluster.ftl +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash -#PBS -q ${clusterqueue} -#PBS -l nodes=1:ppn=${cores} -#PBS -l walltime=${walltime} -#PBS -l mem=${memory}gb -#PBS -e ${location}/err/err_${scriptID}.err -#PBS -o ${location}/out/out_${scriptID}.out -mkdir -p ${location}/err -mkdir -p ${location}/out -printf "${scriptID}_started " >>${location}/log_${jobID}.txt -date "+DATE: %m/%d/%y%tTIME: %H:%M:%S" >>${location}/log_${jobID}.txt -date "+start time: %m/%d/%y%t %H:%M:%S" >>${location}/extra/${scriptID}.txt -echo running on node: `hostname` >>${location}/extra/${scriptID}.txt -${actualcommand} -${verificationcommand} -printf "${scriptID}_finished " >>${location}/log_${jobID}.txt -date "+finish time: %m/%d/%y%t %H:%M:%S" >>${location}/extra/${scriptID}.txt -date "+DATE: %m/%d/%y%tTIME: %H:%M:%S" >>${location}/log_${jobID}.txt diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-download-grid.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-download-grid.ftl deleted file mode 100644 index 8313d2571f..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-download-grid.ftl +++ /dev/null @@ -1,3 +0,0 @@ -#download input data -lcg-cp lfn://grid/lsgrid/${srm_name} \ -file:///$TMPDIR/${just_name} diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-errorfile.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-errorfile.ftl deleted file mode 100644 index cfe02a7a3b..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-errorfile.ftl +++ /dev/null @@ -1 +0,0 @@ -${location}/err/err_${scriptID}.err \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-exe-grid-dir.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-exe-grid-dir.ftl deleted file mode 100644 index e88240aee5..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-exe-grid-dir.ftl +++ /dev/null @@ -1 +0,0 @@ -$TMPDIR/ \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-exe-grid.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-exe-grid.ftl deleted file mode 100644 index 8a21510189..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-exe-grid.ftl +++ /dev/null @@ -1,7 +0,0 @@ -#download executable -lcg-cp lfn://grid/lsgrid/${srm_name} \ -file:///$TMPDIR/${just_name} -chmod 755 $TMPDIR/${just_name} - -/bin/hostname - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-extrafile.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-extrafile.ftl deleted file mode 100644 index f8e1aa3924..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-extrafile.ftl +++ /dev/null @@ -1 +0,0 @@ -${location}/extra/${scriptID}.txt \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-jdl-grid.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-jdl-grid.ftl deleted file mode 100644 index fd157e2060..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-jdl-grid.ftl +++ /dev/null @@ -1,19 +0,0 @@ -Type="Job"; -JobType="Normal"; - -Executable = "/bin/sh"; -Arguments = "${script_name}.sh"; - -StdError = "${error_log}"; -StdOutput = "${output_log}"; - -InputSandbox = {"${script_location}/${script_name}.sh${extra_inputs}"}; -OutputSandbox = {"${error_log}","${output_log}"${extra_outputs}}; - -Requirements = other.GlueCEUniqueID == "ce.grid.rug.nl:8443/cream-pbs-medium" -|| other.GlueCEUniqueID =="gb-ce-tud.ewi.tudelft.nl:8443/cream-pbs-medium" -|| other.GlueCEUniqueID =="gb-ce-nki.els.sara.nl:8443/cream-pbs-medium" -|| other.GlueCEUniqueID =="gb-ce-lumc.lumc.nl:8443/cream-pbs-medium" -|| other.GlueCEUniqueID =="gb-ce-rug.sara.usor.nl:8443/cream-pbs-medium" -|| other.GlueCEUniqueID =="gb-ce-ams.els.sara.nl:8443/cream-pbs-medium" -|| other.GlueCEUniqueID =="creamce.grid.rug.nl:8443/cream-pbs-medium"; diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-logfile.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-logfile.ftl deleted file mode 100644 index 4efcfb97dc..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-logfile.ftl +++ /dev/null @@ -1 +0,0 @@ -${location}/log_${jobID}.txt \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-outfile.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-outfile.ftl deleted file mode 100644 index 8a88f9a640..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-outfile.ftl +++ /dev/null @@ -1 +0,0 @@ -${location}/out/out_${scriptID}.out \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-submit.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-submit.ftl deleted file mode 100644 index d5a5295488..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-submit.ftl +++ /dev/null @@ -1,4 +0,0 @@ -#job_${submitID} -job_${submitID}=$(qsub -N ${scriptID} ${dependancy} ${scriptID}.sh) -echo $job_${submitID} -sleep 8 diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-upload-grid.ftl b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-upload-grid.ftl deleted file mode 100644 index abcdb97d98..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/templates/templ-upload-grid.ftl +++ /dev/null @@ -1,6 +0,0 @@ -#upload result data; -#created an empty file first to avoid uploading error if file is not created -echo -n "" >> file:///$TMPDIR/${just_name} -lcg-cr -l lfn://grid/lsgrid/${srm_name} \ -file:///$TMPDIR/${just_name} - diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/QCworkflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/QCworkflow.csv deleted file mode 100644 index 2a5d401881..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/QCworkflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -QCReport,QCReport, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/create_in-house_ngs_projects_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/create_in-house_ngs_projects_workflow.csv deleted file mode 100644 index 4c8b0e52ae..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/create_in-house_ngs_projects_workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name protocol_name PreviousSteps_name -CreateInhouseProjects CreateInhouseProjects \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/create_in-house_ngs_runs_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/create_in-house_ngs_runs_workflow.csv deleted file mode 100644 index 41e5772cf6..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/create_in-house_ngs_runs_workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -CreateInhouseRuns,CreateInhouseRuns, diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/folding_demo_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/folding_demo_workflow.csv deleted file mode 100644 index 16efe5a2ba..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/folding_demo_workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -MergeBam,MergeBam \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/imputation_demo_parameters.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/imputation_demo_parameters.csv deleted file mode 100644 index 36fc7593be..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/imputation_demo_parameters.csv +++ /dev/null @@ -1,40 +0,0 @@ -Name defaultValue description dataType hasOne_name -mkdir_command srmmkdir The shell command to create directory string -root_dir bbmri.nl/byelas The root directory string -tool_dir ${root_dir}/tools The root directory string -results_dir ${root_dir}/TEST_RESULTS1 Directory where the results will be stored string -study_tped ${root_dir}/GWAS/NLhap550/NLhap550.hg19.tped The path to the TPED file of the study string -study_tfam ${root_dir}/GWAS/NLhap550/NLhap550.hg19.tfam The path to the TFAM fiel of the study string -study_root_basename "${study_tped?substring(0, study_tped?last_index_of('.'))}" The full path without the extension of the study file string -pattern_reference_map ${root_dir}/1000G_genetic_map/genetic_map_chr@CHR@_combined_b37.txt The string pattern of the reference genetic map string -pattern_reference_haps ${root_dir}/reference_dataset/ALL.chr@CHR@.merged_beagle_mach.20101123.snps_indels_svs.genotypes.exported.impute.hap The string pattern of the reference haps string -pattern_reference_legend ${root_dir}/reference_dataset/ALL.chr@CHR@.merged_beagle_mach.20101123.snps_indels_svs.genotypes.exported.impute.legend The string pattern of the reference legend string -reference_base_name "${pattern_reference_haps?replace('@CHR@', chromosome)?substring(pattern_reference_haps?replace('@CHR@', chromosome)?last_index_of('/') + 1 , pattern_reference_haps?replace('@CHR@', chromosome)?last_index_of('.'))}" The basename of the reference string -path_to_beagle2linkage ${tool_dir}/beagle_3.3_26Dec10/beagle2linkage.jar path_to_beagle2linkage string -study_base_name "${study_tped?substring(study_tped?last_index_of('/') + 1 , study_tped?last_index_of('.'))}" The basename of the input study. i.e. the basename of to/path/study.ped is study string -keep_filename ${root_dir}/keep.txt Samples to keep for the analysis string -plink_input_options --tfile ${study_root_basename} <#if (keep_filename?trim?length > 2 )> --keep ${keep_filename} The input parameter for plink string -chromosome Python list of chromosome numbers that the imputation will run string -bin_file bin-bini! string -output_files ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_${start_pos}_${end_pos} ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_5000001_10000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_10000001_15000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_15000001_20000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_20000001_25000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_25000001_30000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_30000001_35000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_35000001_40000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_40000001_45000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_45000001_50000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_50000001_55000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_55000001_60000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_60000001_65000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_65000001_70000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_70000001_75000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_75000001_80000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_80000001_85000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_85000001_90000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_90000001_95000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_95000001_100000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_100000001_105000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_105000001_110000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_110000001_115000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_115000001_120000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_120000001_125000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_125000001_130000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_130000001_135000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_135000001_140000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_140000001_145000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_145000001_150000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_150000001_155000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_155000001_160000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_160000001_165000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_165000001_170000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_170000001_175000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_175000001_180000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_180000001_185000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_185000001_190000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_190000001_195000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_195000001_200000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_200000001_205000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_205000001_210000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_210000001_215000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_215000001_220000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_220000001_225000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_225000001_230000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_230000001_235000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_235000001_240000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_240000001_245000000 ${results_dir}/${reference_base_name}__vs__${study_base_name}_chr${chromosome}/output_chr_${chromosome}pos_245000001_250000000 List of all the final output files of the imputation commands string -path_to_wikipl_scripts ${tool_dir}/python_scripts Path where the python scripts are located string -path_to_beagle ${tool_dir}/beagle_3.3_26Dec10/beagle.jar path_to_beagle string -experiment_name NLhap550_vs_1000G Name of this experiment and directory under temporary files will be stored string -temp_dir ${root_dir}/${experiment_name}/TEMP Temporary directory for intermediate files string -path_to_plink ${tool_dir}/plink-1.07-x86_64/plink-1.07-x86_64/plink path_to_plink string -path_to_linkage2beagle ${tool_dir}/beagle_3.3_26Dec10/linkage2beagle.jar path_to_linkage2beagle string -path_to_impute2 ${tool_dir}/impute_v2.2.2_x86_64_static/impute2 path_to_impute2 string -study_PEDMAP_chr ${temp_dir}/study_PEDMAP_chr${chromosome} The study file of each chromosome string -path_to_gtool ${tool_dir}/gtool_v0.6.6_x86_64/gtool path_to_gtool string -start_pos imputation bp starting position string -end_pos imputation bp ending position strign -scriptName _impute_${reference_base_name}__vs__${study_base_name}_chr${chromosome}_{start_pos}_{end_pos} The name of the output script string -input_1 ${root_dir}/test_dataset/chr${chromosome}.controls.hap550.gen -input_2 "${pattern_reference_haps?replace('@CHR@', chromosome)}" input_2 string -input_3 "${pattern_reference_legend?replace('@CHR@', chromosome)}" input_3 string -input_4 "${pattern_reference_map?replace('@CHR@', chromosome)}" input_4 string -sample_g ${root_dir}/test_dataset/chr${chromosome}.controls.sample -exclude_samples_g ${root_dir}/test_dataset/${bin_file} -sample_g_ref ${temp_dir}/study_GENSAMPLE_norm_chr${chromosome}/sample_exclude_names.txt -output_1 ${results_dir}/test_vs_GoNL_chr${chromosome}_${start_pos}_${end_pos}_${bin_file} output_1 string -log ${results_dir}/test_vs_GoNL_chr${chromosome}_${start_pos}_${end_pos}_${bin_file}.log log string diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/imputation_demo_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/imputation_demo_workflow.csv deleted file mode 100644 index 4e06122a6d..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/imputation_demo_workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name protocol_name PreviousSteps_name -Imputation-processingElement Imputation-processing diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters.csv deleted file mode 100644 index 7e662a2d2f..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters.csv +++ /dev/null @@ -1,264 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,nodes,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -defaultInterpreter,#!/bin/bash,,, -library,${fileprefix},,, -jobname,jobname,,string, -root,/data/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -workflowHeader,NGSHeader.ftl,,, -tooldir,${root}/tools,root dir for tools,string, -gafhome,/target/gpfs2/gaf,gaf home dir,string, -gaftools,${gafhome}/tools,,string, -gafscripts,${gaftools}/scripts,,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -demultiplexWorkflowFile,${McDir}/workflows/in-house_workflow_demultiplex.csv,,string, -workflowFile,${McDir}/workflows/in-house_workflow_realignmentAndSnpCalling.csv,,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R-2.14.2/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -intervallistdir,${resdir}/${genome}/intervals,,, -capturingKit,,,, -baitintervals,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileIDtest}.interval_list,,, -targetintervals,${intervallistdir}/${capturingKit}_exons_${genome}_${indexfileIDtest}.interval_list,,, -baitsbed,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileIDtest}.bed,,, -tempdir,/local,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -datadir,${root}/groups/in-house,root dir for data,string, -allRawNgsDataDir,${datadir}/rawdata/ngs/,"Contains all rawdata (i.e., *.fq files)",string, -allRunDemultiplexDir,${datadir}/runs/,Demultiplex historical data specific runs directory,string, -runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell},,string, -runJobsDir,${allRunDemultiplexDir}/${runPrefix}/jobs/,Run specific job scripts directory,string, -runResultsDir,${allRunDemultiplexDir}/${runPrefix}/results/,Store demultiplexed results here,string, -rawdatadir,${allRawNgsDataDir}/${runPrefix},"contains rawdata (i.e., *.fq files)",string, -arraydir,${datadir}/rawdata/array,,, -fileprefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane},first part of file name,string, -srinputfile,${rawdatadir}/${fileprefix}.fq.gz,use for single read,, -leftinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_1.fq.gz,use as hack to simulate paired end data,, -rightinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_2.fq.gz,use as hack to simulate paired end data,, -leftinputfile,${rawdatadir}/${fileprefix}_1.fq.gz,fastq file with left read of sequence,string, -rightinputfile,${rawdatadir}/${fileprefix}_2.fq.gz,fastq file with right read of sequence,string, -projectdir,${datadir}/projects/${project}/${McId},project folder for this insilico run,, -runtimelog,${projectdir}/${fileprefix}.runtime.log,,, -projectrawdatadir,${projectdir}/rawdata/ngs/,project specific rawdata directory for (demultiplexed) reads,string, -projectrawarraydatadir,${projectdir}/rawdata/array/,"Contains project specific rawdata (i.e., Genome Studio files)",string, -intermediatedir,${projectdir}/intermediate/,store intermediate results here; empty at end of project,, -projectJobsDir,${projectdir}/jobs/,Project specific job scripts directory,string, -projectLogsDir,${projectdir}/logs/,Project specific log directory,string, -projectResultsDir,${projectdir}/results/,Store final results here; a sub set of the primary outputs that we want to keep/archive are moved to this dir; afterwards the remaining files from the intermediate dir will be lost when we clean up.,string, -project,,,,"contact,allRawNgsDataDir" -sequencingStartDate,,,, -sequencer,,,, -run,,,,"sequencer,sequencingStartDate,runJobsDir,runResultsDir" -flowcell,,,,"run,runJobsDir,runResultsDir" -seqType,,,, -lane,,,,"flowcell,seqType" -barcode,,,, -leftbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_1,use these in case of demultiplexed files,, -rightbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_2,idem,, -leftbarcodefq,${leftbarcode}.fq,,, -rightbarcodefq,${rightbarcode}.fq,,, -outputleftright,"${leftbarcodefq},${rightbarcodefq}","file locations for both ends where we save demultiplexed reads, given respecive project folder and barcode",string, -srbarcodefq,${projectrawdatadir}/${fileprefix}_${barcode}.fq,,, -demultiplexinfodir,${datadir}/demultiplexinfo,directory in which we store logs and discarded reads files,string, -logfile,${demultiplexinfodir}/${fileprefix}.log.txt,log file with statistics on demultiplexing process,string, -runtimelogdemultiplex,${demultiplexinfodir}/${fileprefix}.runtime.log,,, -discardleft,${demultiplexinfodir}/${fileprefix}_DISCARD_1.fq,file that contains 'left ends' of sequences with undected barcodes,string, -discardright,${demultiplexinfodir}/${fileprefix}_DISCARD_2.fq,file that contains 'right ends' of sequences with undected barcodes,string, -leftbarcodefqgz,${leftbarcodefq}.gz,"gziped file, in project raw data dir",, -rightbarcodefqgz,${rightbarcodefq}.gz,,, -srbarcodefqgz,${srbarcodefq}.gz,,, -leftfile,${intermediatedir}/${fileprefix}_${barcode}_1,,, -rightfile,${intermediatedir}/${fileprefix}_${barcode}_2,,, -leftfastqczip,${leftfile}_fastqc.zip,(fastqc.ftl),, -rightfastqczip,${rightfile}_fastqc.zip,(fastqc.ftl),, -leftfastqcsummarytxt,${leftfile}_fastqcsummary.txt,(fastqc.ftl),, -rightfastqcsummarytxt,${rightfile}_fastqcsummary.txt,(fastqc.ftl),, -leftfastqcsummarylog,${leftfile}_fastqcsummary.log,(fastqc.ftl),, -rightfastqcsummarylog,${rightfile}_fastqcsummary.log,(fastqc.ftl),, -fastqcjar,${tooldir}/fastqc-v0.7.0/fastqc,(fastqc.ftl),, -leftbwaout,${leftfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -rightbwaout,${rightfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -bwaalignjar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_align),, -bwaaligncores,4,(bwa_align),, -fileWithIndexID,${intermediatedir}/${fileprefix}_${barcode}.${indexfileID},Just a shorthand in this parameters file,, -samfile,${fileWithIndexID}.sam,(bwa_sampe),, -bwasampejar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_sampe),, -bamfile,${fileWithIndexID}.bam,(sam to bam),, -picard,${tooldir}/picard-tools-1.61,,, -samtobamjar,${picard}/SamFormatConverter.jar,,, -sortedbam,${fileWithIndexID}.sorted.bam,,, -sortedbamindex,${fileWithIndexID}.sorted.bam.bai,,, -sortsamjar,${picard}/SortSam.jar,,, -buildbamindexjar,${picard}/BuildBamIndex.jar,,, -alignmentmetricsjar,${picard}/CollectAlignmentSummaryMetrics.jar,,, -alignmentmetrics,${fileWithIndexID}.alignmentmetrics,,, -gcbiasmetricsjar,${picard}/CollectGcBiasMetrics.jar,,, -gcbiasmetrics,${fileWithIndexID}.gcbiasmetrics,,, -gcbiasmetricspdf,${gcbiasmetrics}.pdf,,, -insertsizemetricsjar,${picard}/CollectInsertSizeMetrics.jar,,, -insertsizemetrics,${fileWithIndexID}.insertsizemetrics,,, -insertsizemetricspdf,${insertsizemetrics}.pdf,,, -meanqualitybycyclejar,${picard}/MeanQualityByCycle.jar,,, -meanqualitybycycle,${fileWithIndexID}.meanqualitybycycle,,, -meanqualitybycyclepdf,${fileWithIndexID}.meanqualitybycycle.pdf,,, -qualityscoredistributionjar,${picard}/QualityScoreDistribution.jar,,, -qualityscoredistribution,${fileWithIndexID}.qualityscoredistribution,,, -qualityscoredistributionpdf,${fileWithIndexID}.qualityscoredistribution.pdf,,, -hsmetricsjar,${picard}/CalculateHsMetrics.jar,,, -hsmetrics,${fileWithIndexID}.hsmetrics,,, -bamindexstatsjar,${picard}/BamIndexStats.jar,,, -bamindexstats,${fileWithIndexID}.bamindexstats,(picardQC),, -dedupbam,${fileWithIndexID}.dedup.bam,,, -dedupbamindex,${fileWithIndexID}.dedup.bam.bai,,, -dedupmetrics,${fileWithIndexID}.dedup.metrics,,, -markduplicatesjar,${picard}/MarkDuplicates.jar,,, -dbsnprod,${resdir}/${genome}/dbsnp/dbsnp_129_b37_${indexfileID}.rod,,, -pilot1KgVcf,${resdir}/${genome}/indels/1kg_pilot_release_merged_indels_sites_${genome}_${indexfileID}.vcf,,, -realignTargets,${fileWithIndexID}.realign.target.intervals,,, -genomeAnalysisTKjar,${tooldir}/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar,,, -genomeAnalysisTKjar1411,${tooldir}/GATK-1.4-11-g845c0b1/dist/GenomeAnalysisTK.jar,,, -realignedbam,${fileWithIndexID}.realigned.bam,,, -matefixedbam,${fileWithIndexID}.matefixed.bam,,, -matefixedbamindex,${matefixedbam}.bai,,, -matefixedcovariatecsv,${fileWithIndexID}.matefixed.covariates.table.csv,,, -fixmateinformationjar,${picard}/FixMateInformation.jar,,, -recalbam,${fileWithIndexID}.recal.bam,(samsortrecal),, -sortedrecalbam,${fileWithIndexID}.recal.sorted.bam,(samsortrecal),, -sortedrecalbamindex,${sortedrecalbam}.bai,(samsortrecal),, -mergesamfilesjar,${picard}/MergeSamFiles.jar,(MergeBam),, -externalSampleID,,(MergeBam),,"project,capturingKit,arrayFile,arrayID" -mergedbam,${intermediatedir}/${externalSampleID}.${indexfileID}.merged.bam,(MergeBam),,externalSampleID -mergedbamindex,${mergedbam}.bai,(MergeBam),,mergedbam -sortedrecalcovariatecsv,${fileWithIndexID}.recal.covariate.table.csv,,, -recalstatsbeforedir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.before,,, -recalstatsafterdir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.after,,, -cyclecovariatebefore,${recalstatsbeforedir}/${lane}.CycleCovariate.dat,,, -cyclecovariateafter,${recalstatsafterdir}/${lane}.CycleCovariate.dat,,, -analyzecovariatesjar,${tooldir}/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar,,, -sample,${intermediatedir}/${externalSampleID},(PicardQCRecal),, -samplealignmentmetrics,${sample}.alignmentmetrics,(PicardQCRecal),, -samplegcbiasmetrics,${sample}.gcbiasmetrics,(PicardQCRecal),, -samplegcbiasmetricspdf,${samplegcbiasmetrics}.pdf,(PicardQCRecal),, -sampleinsertsizemetrics,${sample}.insertsizemetrics,(PicardQCRecal),, -sampleinsertsizemetricspdf,${sampleinsertsizemetrics}.pdf,(PicardQCRecal),, -samplemeanqualitybycycle,${sample}.meanqualitybycycle,(PicardQCRecal),, -samplemeanqualitybycyclepdf,${samplemeanqualitybycycle}.pdf,(PicardQCRecal),, -samplequalityscoredistribution,${sample}.qualityscoredistribution,(PicardQCRecal),, -samplequalityscoredistributionpdf,${samplequalityscoredistribution}.pdf,(PicardQCRecal),, -samplebamindexstats,${sample}.bamindexstats.pdf,(PicardQCRecal),, -samplehsmetrics,${sample}.hsmetrics,(PicardQCRecal),, -coveragescript,${tooldir}/coverage_26jan2011/coverage.sh,(Coverage),, -samplecoverageplotpdf,${sample}.coverageplot.pdf,(Coverage),, -coveragegatk,${sample}.coveragegatk,(CoverageGATK),, -cumcoveragescriptgatk,${tooldir}/scripts/plot_cumulative_coverage-1.1.R,(CoverageGATK),, -indelsbed,${sample}.indels.bed,,, -indelsvcf,${sample}.indels.vcf,,, -indelsverboseoutput,${sample}.indels.verboseoutput.txt,,, -filterSingleSampleCallsperl,${tooldir}/scripts/filterSingleSampleCalls.pl,,, -indelsfilteredbed,${sample}.indels.filtered.bed,,, -makeIndelMaskpyton,${tooldir}/scripts/makeIndelMask.py,,, -indelsmaskbed,${sample}.indels.mask.bed,(MakeIndelsMask),, -snpsvcf,${sample}.snps.vcf,,, -snpsvariantannotatedvcf,${sample}.snps.variant.annotated.vcf,,, -annotationPath,${resdir}/${genome}/dbsnp,,, -dbsnpSNPstxt,${annotationPath}/dbSNP135.tabdelim.table,(GenomicAnnotator),, -snpsgenomicannotatedvcf,${sample}.snps.genomic.annotated.vcf,(GenomicAnnotator),, -dbsnpvcf,${annotationPath}/dbsnp_132.b37.vcf,(VariantAnnotator),, -snpeffjar,${tooldir}/snpEff_2_0_5/snpEff.jar,(VariantAnnotator),, -snpeffconfig,${tooldir}/snpEff_2_0_5/snpEff.config,(VariantAnnotator),, -snpeffsummaryhtml,${sample}.snps.final.snpEff_summary.html,(VariantAnnotator),, -snpeffintermediate,${sample}.snps.intermediate.snpEff.vcf,(VariantAnnotator),, -snpsfinal,${sample}.snps.final,(VariantAnnotator),, -snpsfinalvcf,${snpsfinal}.vcf,(VariantAnnotator),, -snpsgenomicannotatedfilteredvcf,${sample}.snps.variant.genomic.annotated.filtered.vcf,(VariantFiltration),, -vcf2tablepy,${tooldir}/GATK-1.0.5069/Sting/python/vcf2table.py,(VcfToTable),, -snpsfinalvcftable,${snpsfinalvcf}.table,(VcfToTable),, -snpannotationstatspl,${tooldir}/scripts/snp_annotation_stats.pl,(VcfToTable),, -createsnptablescriptpath,${tooldir}/scripts/createSNPTable_19mar2012,,, -createsnptablescript,${createsnptablescriptpath}/createSNPTable.R,,, -snpsfinalvcftabletype,${snpsfinal}.type.txt,(VcfToTable),, -snpsfinalvcftableclass,${snpsfinal}.class.txt,(VcfToTable),, -snpsfinalvcftableimpact,${snpsfinal}.impact.txt,(VcfToTable),, -snpstatsprefix,${intermediatedir}/${project}.snps.final,,, -typetableout,${snpstatsprefix}.type.tex,QCReport,, -classtableout,${snpstatsprefix}.class.tex,QCReport,, -impacttableout,${snpstatsprefix}.impact.tex,QCReport,, -arrayFile,,,, -arrayID,,,, -finalreport,${arraydir}/${externalSampleID}_FinalReport.txt,(ConcordanceCheck),, -familylist,${sample}.familylist.txt,(ConcordanceCheck),, -arraytmpmap,${sample}.concordance.tmp.map,(ConcordanceCheck),, -arraymapfile,${sample}.concordance.map,(ConcordanceCheck),, -sampleconcordancefile,${sample}.concordance.ngsVSarray.txt,(ConcordanceCheck),, -getstatisticsscriptpath,${tooldir}/getStatistics_23jan2012,QCStatistics,, -getStatisticsScript,${getstatisticsscriptpath}/getStatistics.R,QCStatistics,, -qcstatisticscolnames,${getstatisticsscriptpath}/NiceColumnNames.csv,QCStatistics,, -gaffig,${getstatisticsscriptpath}/GAFpipeline.png,QCStatistics,, -gccfig,${getstatisticsscriptpath}/Agilent_experiment.png,QCStatistics,, -qcdir,${projectdir}/qc,QCStatistics,, -qcbaitset,${qcdir}/projectbaitset.txt,QCStatistics,, -qcdedupmetricsout,${qcdir}/dedupmetrics.txt,QCStatistics,, -qcstatisticscsv,${qcdir}/${project}_QCStatistics.csv,QCStatistics,, -qcstatisticstex,${qcdir}/${project}_qcstatisticstable.tex,QCStatistics,, -qcstatisticsdescription,${qcdir}/${project}_qcstatisticsdescription.tex,QCStatistics,, -qcstatisticstexreport,${qcdir}/${project}_QCReport.tex,QCStatistics,, -demultiplexstats,${qcdir}/${fileprefix}.log.txt,QCStatistics,, -dot,${tooldir}/graphviz-2.28.0/bin/dot,QCStatistics,, -workflowpng,${qcdir}/${project}_workflow.png,QCStatistics,, -getDedupInfoScript,${scriptdir}/getDedupInfo_23mar2012/getDedupInfo.R,,, -#,,,, -filenamePartSeperator,_,,, -filenamePrefix,${sequencingStartDate}${filenamePartSeperator}${sequencer}${filenamePartSeperator}${run}${filenamePartSeperator}${flowcell}${filenamePartSeperator}L${lane},,string, -fastqExtension,.fq,,string, -gzipExtension,.gz,,string, -md5sumExtension,.md5,,string, -#,,,, -filenameSuffixPE1,1,,, -filenameSuffixPE2,2,,, -filenameSuffixDiscardedReads,DISCARDED,,, -#,,,, -fastqFilenameSR,${filenamePrefix}${fastqExtension},,, -fastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -#,,,, -compressedFastqFilenameSR,${fastqFilenameSR}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE1,${fastqFilenamePE1}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE2,${fastqFilenamePE2}${gzipExtension},use these for multiplexed files,string, -#,,,, -demultiplexedSampleFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilenameSR,${demultiplexedSampleFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilepathSR,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR},,, -compressedDemultiplexedSampleFastqFilepathPE1,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1},,, -compressedDemultiplexedSampleFastqFilepathPE2,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2},,, -#,,,, -demultiplexedSampleFastqChecksumFilenameSR,${demultiplexedSampleFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -log,log.log,,, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_Atabida.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_Atabida.csv deleted file mode 100644 index 53235fb919..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_Atabida.csv +++ /dev/null @@ -1,279 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -demultiplexWorkflowFile,${McDir}/workflows/in-house_workflow_demultiplex.csv,,string, -workflowFile,${McDir}/workflows/in-house_workflow_realignmentAndSnpCallingNonHuman.csv,,string, -genome,at01,,, -indexfileID,Atabida_k77_contigs_no_spaces,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -defaultInterpreter,#!/bin/bash,,, -library,${fileprefix},,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -workflowHeader,NGSHeader.ftl,,, -tooldir,${root}/tools,root dir for tools,string, -gafhome,/target/gpfs2/gaf,gaf home dir,string, -gaftools,${gafhome}/tools,,string, -gafscripts,${gaftools}/scripts,,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R.sh,,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R-2.14.2/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -intervallistdir,${resdir}/${genome}/intervals,,, -capturingKit,,,, -baitintervals,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileID}.interval_list,,, -targetintervals,${intervallistdir}/${capturingKit}_exons_${genome}_${indexfileID}.interval_list,,, -baitsbed,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileID}.bed,,, -tempdir,/target/gpfs2/gcc/tmp,,, -indexfile,${resdir}/${genome}/indices/${indexfileID}.fasta,,, -demultiplexscript,${tooldir}/demultiplex_18oct2011/demultiplex.sh,script for demultiplexing,string, -datadir,${root}/groups/in-house,root dir for data,string, -allRawNgsDataDir,${datadir}/rawdata/ngs/,"Contains all rawdata (i.e., *.fq files)",string, -allRunDemultiplexDir,${datadir}/runs/,Demultiplex historical data specific runs directory,string, -runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell},,string, -runJobsDir,${allRunDemultiplexDir}/${runPrefix}/jobs/,Run specific job scripts directory,string, -runIntermediateDir,${allRunDemultiplexDir}/${runPrefix}/intermediate/,Store demultiplexed results here,string, -rawdatadir,${allRawNgsDataDir}/${runPrefix},"contains rawdata (i.e., *.fq files)",string, -arraydir,${datadir}/rawdata/array,,, -fileprefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane},first part of file name,string, -srinputfile,${rawdatadir}/${fileprefix}.fq.gz,use for single read,, -leftinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_1.fq.gz,use as hack to simulate paired end data,, -rightinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_2.fq.gz,use as hack to simulate paired end data,, -leftinputfile,${rawdatadir}/${fileprefix}_1.fq.gz,fastq file with left read of sequence,string, -rightinputfile,${rawdatadir}/${fileprefix}_2.fq.gz,fastq file with right read of sequence,string, -projectdir,${datadir}/projects/${project}/${McId},project folder for this insilico run,, -runtimelog,${projectdir}/${fileprefix}.runtime.log,,, -projectrawdatadir,${projectdir}/rawdata/ngs/,project specific rawdata directory for (demultiplexed) reads,string, -projectrawarraydatadir,${projectdir}/rawdata/array/,"Contains project specific rawdata (i.e., Genome Studio files)",string, -intermediatedir,${projectdir}/intermediate/,store intermediate results here; empty at end of project,, -projectJobsDir,${projectdir}/jobs/,Project specific job scripts directory,string, -projectLogsDir,${projectdir}/logs/,Project specific log directory,string, -projectResultsDir,${projectdir}/results/,Store final results here; a sub set of the primary outputs that we want to keep/archive are moved to this dir; afterwards the remaining files from the intermediate dir will be lost when we clean up.,string, -project,,,,contact -sequencingStartDate,,,, -sequencer,,,, -run,,,,"sequencer,sequencingStartDate,runJobsDir,runIntermediateDir" -flowcell,,,,"run,runJobsDir,runIntermediateDir" -seqType,,,, -lane,,,,"flowcell,seqType" -barcode,,,, -leftbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_1,use these in case of demultiplexed files,, -rightbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_2,idem,, -leftbarcodefq,${leftbarcode}.fq,,, -rightbarcodefq,${rightbarcode}.fq,,, -outputleftright,"${leftbarcodefq},${rightbarcodefq}","file locations for both ends where we save demultiplexed reads, given respecive project folder and barcode",string, -srbarcodefq,${projectrawdatadir}/${fileprefix}_${barcode}.fq,,, -demultiplexinfodir,${datadir}/demultiplexinfo,directory in which we store logs and discarded reads files,string, -logfile,${demultiplexinfodir}/${fileprefix}.log.txt,log file with statistics on demultiplexing process,string, -runtimelogdemultiplex,${demultiplexinfodir}/${fileprefix}.runtime.log,,, -discardleft,${demultiplexinfodir}/${fileprefix}_DISCARD_1.fq,file that contains 'left ends' of sequences with undected barcodes,string, -discardright,${demultiplexinfodir}/${fileprefix}_DISCARD_2.fq,file that contains 'right ends' of sequences with undected barcodes,string, -leftbarcodefqgz,${leftbarcodefq}.gz,"gziped file, in project raw data dir",, -rightbarcodefqgz,${rightbarcodefq}.gz,,, -srbarcodefqgz,${srbarcodefq}.gz,,, -leftfile,${intermediatedir}/${fileprefix}_${barcode}_1,,, -rightfile,${intermediatedir}/${fileprefix}_${barcode}_2,,, -leftfastqczip,${leftfile}_fastqc.zip,(fastqc.ftl),, -rightfastqczip,${rightfile}_fastqc.zip,(fastqc.ftl),, -leftfastqcsummarytxt,${leftfile}_fastqcsummary.txt,(fastqc.ftl),, -rightfastqcsummarytxt,${rightfile}_fastqcsummary.txt,(fastqc.ftl),, -leftfastqcsummarylog,${leftfile}_fastqcsummary.log,(fastqc.ftl),, -rightfastqcsummarylog,${rightfile}_fastqcsummary.log,(fastqc.ftl),, -fastqcjar,${tooldir}/fastqc-v0.7.0/fastqc,(fastqc.ftl),, -leftbwaout,${leftfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -rightbwaout,${rightfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -bwaalignjar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_align),, -bwaaligncores,4,(bwa_align),, -fileWithIndexID,${intermediatedir}/${fileprefix}_${barcode}.${indexfileID},Just a shorthand in this parameters file,, -samfile,${fileWithIndexID}.sam,(bwa_sampe),, -bwasampejar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_sampe),, -bamfile,${fileWithIndexID}.bam,(sam to bam),, -picard,${tooldir}/picard-tools-1.61,,, -samtobamjar,${picard}/SamFormatConverter.jar,,, -sortedbam,${fileWithIndexID}.sorted.bam,,, -sortedbamindex,${fileWithIndexID}.sorted.bam.bai,,, -sortsamjar,${picard}/SortSam.jar,,, -buildbamindexjar,${picard}/BuildBamIndex.jar,,, -alignmentmetricsjar,${picard}/CollectAlignmentSummaryMetrics.jar,,, -alignmentmetrics,${fileWithIndexID}.alignmentmetrics,,, -gcbiasmetricsjar,${picard}/CollectGcBiasMetrics.jar,,, -gcbiasmetrics,${fileWithIndexID}.gcbiasmetrics,,, -gcbiasmetricspdf,${gcbiasmetrics}.pdf,,, -insertsizemetricsjar,${picard}/CollectInsertSizeMetrics.jar,,, -insertsizemetrics,${fileWithIndexID}.insertsizemetrics,,, -insertsizemetricspdf,${insertsizemetrics}.pdf,,, -meanqualitybycyclejar,${picard}/MeanQualityByCycle.jar,,, -meanqualitybycycle,${fileWithIndexID}.meanqualitybycycle,,, -meanqualitybycyclepdf,${fileWithIndexID}.meanqualitybycycle.pdf,,, -qualityscoredistributionjar,${picard}/QualityScoreDistribution.jar,,, -qualityscoredistribution,${fileWithIndexID}.qualityscoredistribution,,, -qualityscoredistributionpdf,${fileWithIndexID}.qualityscoredistribution.pdf,,, -hsmetricsjar,${picard}/CalculateHsMetrics.jar,,, -hsmetrics,${fileWithIndexID}.hsmetrics,,, -bamindexstatsjar,${picard}/BamIndexStats.jar,,, -bamindexstats,${fileWithIndexID}.bamindexstats,(picardQC),, -dedupbam,${fileWithIndexID}.dedup.bam,,, -dedupbamindex,${fileWithIndexID}.dedup.bam.bai,,, -dedupmetrics,${fileWithIndexID}.dedup.metrics,,, -markduplicatesjar,${picard}/MarkDuplicates.jar,,, -dbsnprod,${resdir}/${genome}/dbsnp/dbsnp_129_b37_${indexfileID}.rod,,, -pilot1KgVcf,${resdir}/${genome}/indels/1kg_pilot_release_merged_indels_sites_${genome}_${indexfileID}.vcf,,, -realignTargets,${fileWithIndexID}.realign.target.intervals,,, -genomeAnalysisTKjar,${tooldir}/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar,,, -genomeAnalysisTKjar1411,${tooldir}/GATK-1.4-11-g845c0b1/dist/GenomeAnalysisTK.jar,,, -realignedbam,${fileWithIndexID}.realigned.bam,,, -matefixedbam,${fileWithIndexID}.matefixed.bam,,, -matefixedbamindex,${matefixedbam}.bai,,, -matefixedcovariatecsv,${fileWithIndexID}.matefixed.covariates.table.csv,,, -fixmateinformationjar,${picard}/FixMateInformation.jar,,, -recalbam,${fileWithIndexID}.recal.bam,(samsortrecal),, -sortedrecalbam,${fileWithIndexID}.recal.sorted.bam,(samsortrecal),, -sortedrecalbamindex,${sortedrecalbam}.bai,(samsortrecal),, -mergesamfilesjar,${picard}/MergeSamFiles.jar,(MergeBam),, -externalSampleID,,(MergeBam),,"project,capturingKit,arrayFile,arrayID" -mergedbam,${intermediatedir}/${externalSampleID}.${indexfileID}.merged.bam,(MergeBam),,externalSampleID -mergedbamindex,${mergedbam}.bai,(MergeBam),,mergedbam -sortedrecalcovariatecsv,${fileWithIndexID}.recal.covariate.table.csv,,, -recalstatsbeforedir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.before,,, -recalstatsafterdir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.after,,, -cyclecovariatebefore,${recalstatsbeforedir}/${lane}.CycleCovariate.dat,,, -cyclecovariateafter,${recalstatsafterdir}/${lane}.CycleCovariate.dat,,, -analyzecovariatesjar,${tooldir}/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar,,, -sample,${intermediatedir}/${externalSampleID},(PicardQCRecal),, -samplealignmentmetrics,${sample}.alignmentmetrics,(PicardQCRecal),, -samplegcbiasmetrics,${sample}.gcbiasmetrics,(PicardQCRecal),, -samplegcbiasmetricspdf,${samplegcbiasmetrics}.pdf,(PicardQCRecal),, -sampleinsertsizemetrics,${sample}.insertsizemetrics,(PicardQCRecal),, -sampleinsertsizemetricspdf,${sampleinsertsizemetrics}.pdf,(PicardQCRecal),, -samplemeanqualitybycycle,${sample}.meanqualitybycycle,(PicardQCRecal),, -samplemeanqualitybycyclepdf,${samplemeanqualitybycycle}.pdf,(PicardQCRecal),, -samplequalityscoredistribution,${sample}.qualityscoredistribution,(PicardQCRecal),, -samplequalityscoredistributionpdf,${samplequalityscoredistribution}.pdf,(PicardQCRecal),, -samplebamindexstats,${sample}.bamindexstats.pdf,(PicardQCRecal),, -samplehsmetrics,${sample}.hsmetrics,(PicardQCRecal),, -coveragescript,${tooldir}/coverage_26jan2011/coverage.sh,(Coverage),, -samplecoverageplotpdf,${sample}.coverageplot.pdf,(Coverage),, -coveragegatk,${sample}.coveragegatk,(CoverageGATK),, -cumcoveragescriptgatk,${tooldir}/scripts/plot_cumulative_coverage-1.1.R,(CoverageGATK),, -indelsbed,${sample}.indels.bed,,, -indelsvcf,${sample}.indels.vcf,,, -indelsverboseoutput,${sample}.indels.verboseoutput.txt,,, -filterSingleSampleCallsperl,${tooldir}/scripts/filterSingleSampleCalls.pl,,, -indelsfilteredbed,${sample}.indels.filtered.bed,,, -makeIndelMaskpyton,${tooldir}/scripts/makeIndelMask.py,,, -indelsmaskbed,${sample}.indels.mask.bed,(MakeIndelsMask),, -snpsvcf,${sample}.snps.vcf,,, -snpsvariantannotatedvcf,${sample}.snps.variant.annotated.vcf,,, -annotationPath,${resdir}/${genome}/dbsnp,,, -dbsnpSNPstxt,${annotationPath}/dbSNP132.tabdelim.table,(GenomicAnnotator),, -snpsgenomicannotatedvcf,${sample}.snps.genomic.annotated.vcf,(GenomicAnnotator),, -dbsnpvcf,${annotationPath}/dbsnp_132.b37.vcf,(VariantAnnotator),, -snpeffjar,${tooldir}/snpEff_2_0_5/snpEff.jar,(VariantAnnotator),, -snpeffconfig,${tooldir}/snpEff_2_0_5/snpEff.config,(VariantAnnotator),, -snpeffsummaryhtml,${sample}.snps.final.snpEff_summary.html,(VariantAnnotator),, -snpeffintermediate,${sample}.snps.intermediate.snpEff.vcf,(VariantAnnotator),, -snpsfinal,${sample}.snps.final,(VariantAnnotator),, -snpsfinalvcf,${snpsfinal}.vcf,(VariantAnnotator),, -snpsgenomicannotatedfilteredvcf,${sample}.snps.variant.genomic.annotated.filtered.vcf,(VariantFiltration),, -vcf2tablepy,${tooldir}/GATK-1.0.5069/Sting/python/vcf2table.py,(VcfToTable),, -snpsfinalvcftable,${snpsfinalvcf}.table,(VcfToTable),, -snpannotationstatspl,${tooldir}/scripts/snp_annotation_stats.pl,(VcfToTable),, -createsnptablescriptpath,${tooldir}/scripts/createSNPTable_19mar2012,,, -createsnptablescript,${createsnptablescriptpath}/createSNPTable.R,,, -snpsfinalvcftabletype,${snpsfinal}.type.txt,(VcfToTable),, -snpsfinalvcftableclass,${snpsfinal}.class.txt,(VcfToTable),, -snpsfinalvcftableimpact,${snpsfinal}.impact.txt,(VcfToTable),, -snpstatsprefix,${intermediatedir}/${project}.snps.final,,, -typetableout,${snpstatsprefix}.type.tex,QCReport,, -classtableout,${snpstatsprefix}.class.tex,QCReport,, -impacttableout,${snpstatsprefix}.impact.tex,QCReport,, -arrayFile,,,, -arrayID,,,, -arrayfilelocation,${arraydir}/${arrayFile}_FinalReport.txt,(ConcordanceCheck),, -finalreport,${sample}.finalreport.txt,(ConcordanceCheck),, -familylist,${sample}.familylist.txt,(ConcordanceCheck),, -arraytmpmap,${sample}.concordance.tmp.map,(ConcordanceCheck),, -arraymapfile,${sample}.concordance.map,(ConcordanceCheck),, -sampleconcordancefile,${sample}.concordance.ngsVSarray.txt,(ConcordanceCheck),, -getstatisticsscriptpath,${tooldir}/getStatistics_23jan2012,QCStatistics,, -getStatisticsScript,${getstatisticsscriptpath}/getStatistics.R,QCStatistics,, -qcstatisticscolnames,${getstatisticsscriptpath}/NiceColumnNames.csv,QCStatistics,, -gaffig,${getstatisticsscriptpath}/GAFpipeline.png,QCStatistics,, -gccfig,${getstatisticsscriptpath}/Agilent_experiment.png,QCStatistics,, -qcdir,${projectdir}/qc,QCStatistics,, -qcbaitset,${qcdir}/projectbaitset.txt,QCStatistics,, -qcdedupmetricsout,${qcdir}/dedupmetrics.txt,QCStatistics,, -qcstatisticscsv,${qcdir}/${project}_QCStatistics.csv,QCStatistics,, -qcstatisticstex,${qcdir}/${project}_qcstatisticstable.tex,QCStatistics,, -qcstatisticsdescription,${qcdir}/${project}_qcstatisticsdescription.tex,QCStatistics,, -qcstatisticstexreport,${qcdir}/${project}_QCReport.tex,QCStatistics,, -demultiplexstats,${qcdir}/${fileprefix}.log.txt,QCStatistics,, -dot,${tooldir}/graphviz-2.28.0/bin/dot,QCStatistics,, -workflowpng,${qcdir}/${project}_workflow.png,QCStatistics,, -getDedupInfoScript,${scriptdir}/getDedupInfo_23mar2012/getDedupInfo.R,,, -# -filenamePartSeperator,_,,, -filenamePrefix,${sequencingStartDate}${filenamePartSeperator}${sequencer}${filenamePartSeperator}${run}${filenamePartSeperator}${flowcell}${filenamePartSeperator}L${lane},,string -fastqExtension,.fq,,string, -gzipExtension,.gz,,string, -md5sumExtension,.md5,,string, -# -filenameSuffixPE1,1,,, -filenameSuffixPE2,2,,, -filenameSuffixDiscardedReads,DISCARDED,,, -# -fastqFilenameSR,${filenamePrefix}${fastqExtension},,, -fastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -# -compressedFastqFilepathSR,${allRawNgsDataDir}/${runPrefix}/${fastqFilenameSR}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilepathPE1,${allRawNgsDataDir}/${runPrefix}/${fastqFilenamePE1}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilepathPE2,${allRawNgsDataDir}/${runPrefix}/${fastqFilenamePE2}${gzipExtension},use these for multiplexed files,string, -# -demultiplexedSampleFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -# -compressedDemultiplexedSampleFastqFilepathSR,${runIntermediateDir}${demultiplexedSampleFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilepathPE1,${runIntermediateDir}${demultiplexedSampleFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilepathPE2,${runIntermediateDir}${demultiplexedSampleFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilepathSR,${runIntermediateDir}${demultiplexedDiscardedFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilepathPE1,${runIntermediateDir}${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilepathPE2,${runIntermediateDir}${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -# -demultiplexedSampleFastqChecksumFilepathSR,${runIntermediateDir}${demultiplexedSampleFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilepathPE1,${runIntermediateDir}${demultiplexedSampleFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilepathPE2,${runIntermediateDir}${demultiplexedSampleFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilepathSR,${runIntermediateDir}${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilepathPE1,${runIntermediateDir}${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilepathPE2,${runIntermediateDir}${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -# -fq_extension,.fq,,string, -gz_extension,.gz,,string, -md5sum_extension,.md5,,string, -fq_gz,${allRawNgsDataDir}/${runPrefix}/${fileprefix}${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_1,${allRawNgsDataDir}/${runPrefix}/${fileprefix}_1${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_2,${allRawNgsDataDir}/${runPrefix}/${fileprefix}_2${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_barcode,${runIntermediateDir}/${fileprefix}_${barcode}${fq_extension},use these in case of demultiplexed files,string, -fq_barcode_1,${runIntermediateDir}/${fileprefix}_${barcode}_1${fq_extension},use these in case of demultiplexed files,string, -fq_barcode_2,${runIntermediateDir}/${fileprefix}_${barcode}_2${fq_extension},use these in case of demultiplexed files,string, -fq_discarded,${runIntermediateDir}/${fileprefix}_DISCARDED${fq_extension},use these in case of demultiplexed files,string, -fq_discarded_1,${runIntermediateDir}/${fileprefix}_DISCARDED_1${fq_extension},use these in case of demultiplexed files,string, -fq_discarded_2,${runIntermediateDir}/${fileprefix}_DISCARDED_2${fq_extension},use these in case of demultiplexed files,string, -fq_gz_barcode,${runIntermediateDir}/${fileprefix}_${barcode}${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_barcode_1,${runIntermediateDir}/${fileprefix}_${barcode}_1${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_barcode_2,${runIntermediateDir}/${fileprefix}_${barcode}_2${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_discarded,${runIntermediateDir}/${fileprefix}_DISCARDED${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_discarded_1,${runIntermediateDir}/${fileprefix}_DISCARDED_1${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -fq_gz_discarded_2,${runIntermediateDir}/${fileprefix}_DISCARDED_2${fq_extension}${gz_extension},use these in case of demultiplexed files,string, -log,log.log,,, diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_gpfs.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_gpfs.csv deleted file mode 100644 index 2801e571d2..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_gpfs.csv +++ /dev/null @@ -1,272 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -defaultInterpreter,#!/bin/bash,,, -library,${fileprefix},,, -jobname,jobname,,string, -root,/target/gpfs2/gcc,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -workflowHeader,NGSHeader.ftl,,, -tooldir,${root}/tools,root dir for tools,string, -gafhome,/target/gpfs2/gaf,gaf home dir,string, -gaftools,${gafhome}/tools,,string, -gafscripts,${gaftools}/scripts,,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${gafscripts}/demultiplex.R,,string, -demultiplexWorkflowFile,${McDir}/workflows/in-house_workflow_demultiplex.csv,,string, -workflowFile,${McDir}/workflows/in-house_workflow_realignmentAndSnpCalling.csv,,string, -resdir,${root}/resources,,, -JAVA_HOME,/cm/shared/apps/sunjdk/jdk1.6.0_21/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -R_LIBS,${tooldir}/GATK-1.3-24-gc8b1c92/gsalib/,,, -intervallistdir,${resdir}/${genome}/intervals,,, -capturingKit,,,, -baitintervals,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileIDtest}.interval_list,,, -targetintervals,${intervallistdir}/${capturingKit}_exons_${genome}_${indexfileIDtest}.interval_list,,, -baitsbed,${intervallistdir}/${capturingKit}_baits_${genome}_${indexfileIDtest}.bed,,, -tempdir,/target/gpfs2/gcc/tmp/processing,,, -tempprojectdir,/target/gpfs2/gcc/tmp,,, -genome,hg19,,, -indexfileID,human_g1k_v37,,, -indexfileIDtest,human_g1k_v37,Append .chr1 if you want to test only on chr 1,, -indexfile,${resdir}/${genome}/indices/${indexfileIDtest}.fa,,, -datadir,${root}/groups/in-house,root dir for data,string, -allRawNgsDataDir,${datadir}/rawdata/ngs/,"Contains all rawdata (i.e., *.fq files)",string, -allRunDemultiplexDir,${datadir}/runs/,Demultiplex historical data specific runs directory,string, -runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell},,string, -runJobsDir,${allRunDemultiplexDir}/${runPrefix}/jobs/,Run specific job scripts directory,string, -runResultsDir,${allRunDemultiplexDir}/${runPrefix}/results/,Store demultiplexed results here,string, -rawdatadir,${allRawNgsDataDir}/${runPrefix},"contains rawdata (i.e., *.fq files)",string, -arraydir,${datadir}/rawdata/array,,, -fileprefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane},first part of file name,string, -srinputfile,${rawdatadir}/${fileprefix}.fq.gz,use for single read,, -leftinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_1.fq.gz,use as hack to simulate paired end data,, -rightinputfileSR,${demultiplexinfodir}/${fileprefix}_SingleRead_2.fq.gz,use as hack to simulate paired end data,, -leftinputfile,${rawdatadir}/${fileprefix}_1.fq.gz,fastq file with left read of sequence,string, -rightinputfile,${rawdatadir}/${fileprefix}_2.fq.gz,fastq file with right read of sequence,string, -projectdir,${datadir}/projects/${project}/${McId},project folder for this insilico run,, -runtimelog,${projectdir}/${fileprefix}.runtime.log,,, -projectrawdatadir,${projectdir}/rawdata/ngs/,project specific rawdata directory for (demultiplexed) reads,string, -projectrawarraydatadir,${projectdir}/rawdata/array/,"Contains project specific rawdata (i.e., Genome Studio files)",string, -intermediatedir,${tempprojectdir}/${project}/${McId}/,store intermediate results here; empty at end of project,, -projectJobsDir,${projectdir}/jobs/,Project specific job scripts directory,string, -projectLogsDir,${projectdir}/logs/,Project specific log directory,string, -projectResultsDir,${projectdir}/results/,Store final results here; a sub set of the primary outputs that we want to keep/archive are moved to this dir; afterwards the remaining files from the intermediate dir will be lost when we clean up.,string, -project,,,,"contact,allRawNgsDataDir" -sequencingStartDate,,,, -sequencer,,,, -run,,,,"sequencer,sequencingStartDate,runJobsDir,runResultsDir" -flowcell,,,,"run,runJobsDir,runResultsDir" -seqType,,,, -lane,,,,"flowcell,seqType" -barcode,,,, -leftbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_1,use these in case of demultiplexed files,, -rightbarcode,${projectrawdatadir}/${fileprefix}_${barcode}_2,idem,, -leftbarcodefq,${leftbarcode}.fq,,, -rightbarcodefq,${rightbarcode}.fq,,, -outputleftright,"${leftbarcodefq},${rightbarcodefq}","file locations for both ends where we save demultiplexed reads, given respecive project folder and barcode",string, -srbarcodefq,${projectrawdatadir}/${fileprefix}_${barcode}.fq,,, -demultiplexinfodir,${datadir}/demultiplexinfo,directory in which we store logs and discarded reads files,string, -logfile,${demultiplexinfodir}/${fileprefix}.log.txt,log file with statistics on demultiplexing process,string, -runtimelogdemultiplex,${demultiplexinfodir}/${fileprefix}.runtime.log,,, -discardleft,${demultiplexinfodir}/${fileprefix}_DISCARD_1.fq,file that contains 'left ends' of sequences with undected barcodes,string, -discardright,${demultiplexinfodir}/${fileprefix}_DISCARD_2.fq,file that contains 'right ends' of sequences with undected barcodes,string, -leftbarcodefqgz,${leftbarcodefq}.gz,"gziped file, in project raw data dir",, -rightbarcodefqgz,${rightbarcodefq}.gz,,, -srbarcodefqgz,${srbarcodefq}.gz,,, -leftfile,${intermediatedir}/${fileprefix}_${barcode}_1,,, -rightfile,${intermediatedir}/${fileprefix}_${barcode}_2,,, -leftfastqczip,${leftfile}.fq_fastqc.zip,(fastqc.ftl),, -rightfastqczip,${rightfile}.fq_fastqc.zip,(fastqc.ftl),, -leftfastqcsummarytxt,${leftfile}_fastqcsummary.txt,(fastqc.ftl),, -rightfastqcsummarytxt,${rightfile}_fastqcsummary.txt,(fastqc.ftl),, -leftfastqcsummarylog,${leftfile}_fastqcsummary.log,(fastqc.ftl),, -rightfastqcsummarylog,${rightfile}_fastqcsummary.log,(fastqc.ftl),, -fastqcjar,${tooldir}/fastqc-v0.7.0/fastqc,(fastqc.ftl),, -leftbwaout,${leftfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -rightbwaout,${rightfile}.bwa_align.${indexfileID}.sai,(bwa_align),, -bwaalignjar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_align),, -bwaaligncores,4,(bwa_align),, -fileWithIndexID,${intermediatedir}/${fileprefix}_${barcode}.${indexfileID},Just a shorthand in this parameters file,, -samfile,${fileWithIndexID}.sam,(bwa_sampe),, -bwasampejar,${tooldir}/bwa-0.5.8c_patched/bwa,(bwa_sampe),, -bamfile,${fileWithIndexID}.bam,(sam to bam),, -picard,${tooldir}/picard-tools-1.61,,, -samtobamjar,${picard}/SamFormatConverter.jar,,, -sortedbam,${fileWithIndexID}.sorted.bam,,, -sortedbamindex,${fileWithIndexID}.sorted.bam.bai,,, -sortsamjar,${picard}/SortSam.jar,,, -buildbamindexjar,${picard}/BuildBamIndex.jar,,, -alignmentmetricsjar,${picard}/CollectAlignmentSummaryMetrics.jar,,, -alignmentmetrics,${fileWithIndexID}.alignmentmetrics,,, -gcbiasmetricsjar,${picard}/CollectGcBiasMetrics.jar,,, -gcbiasmetrics,${fileWithIndexID}.gcbiasmetrics,,, -gcbiasmetricspdf,${gcbiasmetrics}.pdf,,, -insertsizemetricsjar,${picard}/CollectInsertSizeMetrics.jar,,, -insertsizemetrics,${fileWithIndexID}.insertsizemetrics,,, -insertsizemetricspdf,${insertsizemetrics}.pdf,,, -recreateinsertsizepdfR,${tooldir}/createInsertSizePlot/createInsertSizePlot.R,Recreate the insert size pdf's with R,, -meanqualitybycyclejar,${picard}/MeanQualityByCycle.jar,,, -meanqualitybycycle,${fileWithIndexID}.meanqualitybycycle,,, -meanqualitybycyclepdf,${fileWithIndexID}.meanqualitybycycle.pdf,,, -qualityscoredistributionjar,${picard}/QualityScoreDistribution.jar,,, -qualityscoredistribution,${fileWithIndexID}.qualityscoredistribution,,, -qualityscoredistributionpdf,${fileWithIndexID}.qualityscoredistribution.pdf,,, -hsmetricsjar,${picard}/CalculateHsMetrics.jar,,, -hsmetrics,${fileWithIndexID}.hsmetrics,,, -bamindexstatsjar,${picard}/BamIndexStats.jar,,, -bamindexstats,${fileWithIndexID}.bamindexstats,(picardQC),, -dedupbam,${fileWithIndexID}.dedup.bam,,, -dedupbamindex,${fileWithIndexID}.dedup.bam.bai,,, -dedupmetrics,${fileWithIndexID}.dedup.metrics,,, -markduplicatesjar,${picard}/MarkDuplicates.jar,,, -dbsnprod,${resdir}/${genome}/dbsnp/dbsnp_129_b37_${indexfileID}.rod,,, -pilot1KgVcf,${resdir}/${genome}/indels/1kg_pilot_release_merged_indels_sites_${genome}_${indexfileID}.vcf,,, -realignTargets,${fileWithIndexID}.realign.target.intervals,,, -genomeAnalysisTKjar,${tooldir}/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar,,, -genomeAnalysisTKjar1411,${tooldir}/GATK-1.4-11-g845c0b1/dist/GenomeAnalysisTK.jar,,, -realignedbam,${fileWithIndexID}.realigned.bam,,, -matefixedbam,${fileWithIndexID}.matefixed.bam,,, -matefixedbamindex,${matefixedbam}.bai,,, -matefixedcovariatecsv,${fileWithIndexID}.matefixed.covariates.table.csv,,, -fixmateinformationjar,${picard}/FixMateInformation.jar,,, -recalbam,${fileWithIndexID}.recal.bam,(samsortrecal),, -sortedrecalbam,${fileWithIndexID}.recal.sorted.bam,(samsortrecal),, -sortedrecalbamindex,${sortedrecalbam}.bai,(samsortrecal),, -mergesamfilesjar,${picard}/MergeSamFiles.jar,(MergeBam),, -externalSampleID,,(MergeBam),,"project,capturingKit,arrayFile,arrayID" -mergedbam,${intermediatedir}/${externalSampleID}.${indexfileID}.merged.bam,(MergeBam),,externalSampleID -mergedbamindex,${mergedbam}.bai,(MergeBam),,mergedbam -sortedrecalcovariatecsv,${fileWithIndexID}.recal.covariate.table.csv,,, -recalstatsbeforedir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.before,,, -recalstatsafterdir,${intermediatedir}/${fileprefix}_${barcode}.recal.stats.after,,, -cyclecovariatebefore,${recalstatsbeforedir}/${lane}.CycleCovariate.dat,,, -cyclecovariateafter,${recalstatsafterdir}/${lane}.CycleCovariate.dat,,, -analyzecovariatesjar,${tooldir}/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar,,, -sample,${intermediatedir}/${externalSampleID},(PicardQCRecal),, -samplealignmentmetrics,${sample}.alignmentmetrics,(PicardQCRecal),, -samplegcbiasmetrics,${sample}.gcbiasmetrics,(PicardQCRecal),, -samplegcbiasmetricspdf,${samplegcbiasmetrics}.pdf,(PicardQCRecal),, -sampleinsertsizemetrics,${sample}.insertsizemetrics,(PicardQCRecal),, -sampleinsertsizemetricspdf,${sampleinsertsizemetrics}.pdf,(PicardQCRecal),, -samplemeanqualitybycycle,${sample}.meanqualitybycycle,(PicardQCRecal),, -samplemeanqualitybycyclepdf,${samplemeanqualitybycycle}.pdf,(PicardQCRecal),, -samplequalityscoredistribution,${sample}.qualityscoredistribution,(PicardQCRecal),, -samplequalityscoredistributionpdf,${samplequalityscoredistribution}.pdf,(PicardQCRecal),, -samplebamindexstats,${sample}.bamindexstats.pdf,(PicardQCRecal),, -samplehsmetrics,${sample}.hsmetrics,(PicardQCRecal),, -coveragescript,${scriptdir}/coverage.R,(Coverage),, -samplecoverageplotpdf,${sample}.coverageplot.pdf,(Coverage),, -coveragegatk,${sample}.coveragegatk,(CoverageGATK),, -cumcoveragescriptgatk,${tooldir}/scripts/plot_cumulative_coverage-1.1.R,(CoverageGATK),, -indelsbed,${sample}.indels.bed,,, -indelsvcf,${sample}.indels.vcf,,, -indelsverboseoutput,${sample}.indels.verboseoutput.txt,,, -filterSingleSampleCallsperl,${tooldir}/scripts/filterSingleSampleCalls.pl,,, -indelsfilteredbed,${sample}.indels.filtered.bed,,, -makeIndelMaskpyton,${tooldir}/scripts/makeIndelMask.py,,, -indelsmaskbed,${sample}.indels.mask.bed,(MakeIndelsMask),, -snpsvcf,${sample}.snps.vcf,,, -snpsvariantannotatedvcf,${sample}.snps.variant.annotated.vcf,,, -annotationPath,${resdir}/${genome}/dbsnp,,, -dbsnpSNPstxt,${annotationPath}/dbSNP135.tabdelim.table,(GenomicAnnotator),, -snpsgenomicannotatedvcf,${sample}.snps.genomic.annotated.vcf,(GenomicAnnotator),, -dbsnpvcf,${annotationPath}/dbsnp_135.b37.vcf,(VariantAnnotator),, -dbsnpexsitesafter129vcf,${annotationPath}/dbsnp_135.b37.excluding_sites_after_129.vcf,(ConcordanceCheck),, -snpeffjar,${tooldir}/snpEff_2_0_5/snpEff.jar,(VariantAnnotator),, -snpeffconfig,${tooldir}/snpEff_2_0_5/snpEff.config,(VariantAnnotator),, -snpeffsummaryhtml,${sample}.snps.final.snpEff_summary.html,(VariantAnnotator),, -snpeffintermediate,${sample}.snps.intermediate.snpEff.vcf,(VariantAnnotator),, -snpsfinal,${sample}.snps.final,(VariantAnnotator),, -snpsfinalvcf,${snpsfinal}.vcf,(VariantAnnotator),, -snpsgenomicannotatedfilteredvcf,${sample}.snps.variant.genomic.annotated.filtered.vcf,(VariantFiltration),, -vcf2tablepy,${tooldir}/GATK-1.0.5069/Sting/python/vcf2table.py,(VcfToTable),, -snpsfinalvcftable,${snpsfinalvcf}.table,(VcfToTable),, -snpannotationstatspl,${tooldir}/scripts/snp_annotation_stats.pl,(VcfToTable),, -createsnptablescriptpath,${tooldir}/scripts/createSNPTable_19mar2012,,, -createsnptablescript,${createsnptablescriptpath}/createSNPTable.R,,, -snpsfinalvcftabletype,${snpsfinal}.type.txt,(VcfToTable),, -snpsfinalvcftableclass,${snpsfinal}.class.txt,(VcfToTable),, -snpsfinalvcftableimpact,${snpsfinal}.impact.txt,(VcfToTable),, -snpstatsprefix,${intermediatedir}/${project}.snps.final,,, -typetableout,${snpstatsprefix}.type.tex,QCReport,, -classtableout,${snpstatsprefix}.class.tex,QCReport,, -impacttableout,${snpstatsprefix}.impact.tex,QCReport,, -arrayFile,,,, -arrayID,,,, -finalreport,${arraydir}/${externalSampleID}_FinalReport.txt,(ConcordanceCheck),, -finalreporttmpdir,${intermediatedir}/${externalSampleID}_FinalReport.txt,(ConcordanceCheck),, -familylist,${sample}.familylist.txt,(ConcordanceCheck),, -arraytmpmap,${sample}.concordance.tmp.map,(ConcordanceCheck),, -arraymapfile,${sample}.concordance.map,(ConcordanceCheck),, -sampleconcordancefile,${sample}.concordance.ngsVSarray.txt,(ConcordanceCheck),, -getstatisticsscriptpath,${tooldir}/getStatistics_23jan2012,QCStatistics,, -getStatisticsScript,${getstatisticsscriptpath}/getStatistics.R,QCStatistics,, -qcstatisticscolnames,${getstatisticsscriptpath}/NiceColumnNames.csv,QCStatistics,, -gaffig,${getstatisticsscriptpath}/GAFpipeline.png,QCStatistics,, -gccfig,${getstatisticsscriptpath}/Agilent_experiment.png,QCStatistics,, -qcdir,${projectdir}/qc,QCStatistics,, -qcbaitset,${qcdir}/projectbaitset.txt,QCStatistics,, -qcdedupmetricsout,${qcdir}/dedupmetrics.txt,QCStatistics,, -qcstatisticscsv,${qcdir}/${project}_QCStatistics.csv,QCStatistics,, -qcstatisticstex,${qcdir}/${project}_qcstatisticstable.tex,QCStatistics,, -qcstatisticsdescription,${qcdir}/${project}_qcstatisticsdescription.tex,QCStatistics,, -qcstatisticstexreport,${qcdir}/${project}_QCReport.tex,QCStatistics,, -demultiplexstats,${qcdir}/${fileprefix}.log.txt,QCStatistics,, -dot,${tooldir}/graphviz-2.28.0/bin/dot,QCStatistics,, -workflowpng,${qcdir}/${project}_workflow.png,QCStatistics,, -getDedupInfoScript,${scriptdir}/getDedupInfo_23mar2012/getDedupInfo.R,,, -#,,,, -filenamePartSeperator,_,,, -filenamePrefix,${sequencingStartDate}${filenamePartSeperator}${sequencer}${filenamePartSeperator}${run}${filenamePartSeperator}${flowcell}${filenamePartSeperator}L${lane},,string, -fastqExtension,.fq,,string, -gzipExtension,.gz,,string, -md5sumExtension,.md5,,string, -#,,,, -filenameSuffixPE1,1,,, -filenameSuffixPE2,2,,, -filenameSuffixDiscardedReads,DISCARDED,,, -#,,,, -fastqFilenameSR,${filenamePrefix}${fastqExtension},,, -fastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -#,,,, -fastqChecksumFilenameSR,${fastqFilenameSR}${md5sumExtension},,, -fastqChecksumFilenamePE1,${fastqFilenamePE1}${md5sumExtension},,, -fastqChecksumFilenamePE2,${fastqFilenamePE1}${md5sumExtension},,, -#,,,, -compressedFastqFilenameSR,${fastqFilenameSR}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE1,${fastqFilenamePE1}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE2,${fastqFilenamePE2}${gzipExtension},use these for multiplexed files,string, -#,,,, -demultiplexedSampleFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilenameSR,${demultiplexedSampleFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilepathSR,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR},,, -compressedDemultiplexedSampleFastqFilepathPE1,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1},,, -compressedDemultiplexedSampleFastqFilepathPE2,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2},,, -#,,,, -demultiplexedSampleFastqChecksumFilenameSR,${demultiplexedSampleFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -log,log.log,,, diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_pipeline.target.rug.nl.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_pipeline.target.rug.nl.csv deleted file mode 100644 index c8e0515e87..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_parameters_pipeline.target.rug.nl.csv +++ /dev/null @@ -1,85 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -clusterQueue,umcg,,, -mem,4,Memory in GB,, -walltime,23:59:00,,, -cores,1,,, -defaultInterpreter,#!/bin/bash,,, -library,${fileprefix},,, -jobname,jobname,,string, -root,/scratch1,the root to your tools and data,string, -bashrc,${root}/gcc.bashrc,,, -workflowHeader,NGSHeader.ftl,,, -tooldir,${root}/tools,root dir for tools,string, -gafhome,/scratch1,gaf home dir,string, -gaftools,${gafhome}/tools,,string, -gafscripts,${gaftools}/scripts,,string, -scriptdir,${tooldir}/scripts,,, -importscript,${scriptdir}/import.sh,,, -demultiplexscript,${scriptdir}/demultiplex.R,,string, -demultiplexWorkflowFile,${McDir}/workflows/in-house_workflow_demultiplex.csv,,string, -JAVA_HOME,/target/gpfs2/gcc/tools/jdk/,,, -R_HOME,${tooldir}/R/,,, -R,${R_HOME}/bin/R,,, -rscript,${R_HOME}/bin/Rscript,,, -datadir,${root}/groups/in-house,root dir for data,string, -allRawNgsDataDir,${datadir}/rawdata/ngs/,"Contains all rawdata (i.e., *.fq files)",string, -allRunDemultiplexDir,${datadir}/runs/,Demultiplex historical data specific runs directory,string, -runPrefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell},,string, -runJobsDir,${allRunDemultiplexDir}/${runPrefix}/jobs/,Run specific job scripts directory,string, -runResultsDir,${allRunDemultiplexDir}/${runPrefix}/results/,Store demultiplexed results here,string, -rawdatadir,${allRawNgsDataDir}/${runPrefix},"contains rawdata (i.e., *.fq files)",string, -arraydir,${datadir}/rawdata/array,,, -fileprefix,${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane},first part of file name,string, -sequencingStartDate,,,, -sequencer,,,, -run,,,,"sequencer,sequencingStartDate,runJobsDir,runResultsDir" -flowcell,,,,"run,runJobsDir,runResultsDir" -seqType,,,, -lane,,,,"flowcell,seqType" -barcode,,,, -file,, -#,,,, -filenamePartSeperator,_,,, -filenamePrefix,${sequencingStartDate}${filenamePartSeperator}${sequencer}${filenamePartSeperator}${run}${filenamePartSeperator}${flowcell}${filenamePartSeperator}L${lane},,string, -fastqExtension,.fq,,string, -gzipExtension,.gz,,string, -md5sumExtension,.md5,,string, -#,,,, -filenameSuffixPE1,1,,, -filenameSuffixPE2,2,,, -filenameSuffixDiscardedReads,DISCARDED,,, -#,,,, -fastqFilenameSR,${filenamePrefix}${fastqExtension},,, -fastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},,, -fastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},,, -#,,,, -compressedFastqFilenameSR,${fastqFilenameSR}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE1,${fastqFilenamePE1}${gzipExtension},use these for multiplexed files,string, -compressedFastqFilenamePE2,${fastqFilenamePE2}${gzipExtension},use these for multiplexed files,string, -#,,,, -demultiplexedSampleFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${barcode}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${barcode}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenameSR,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE1,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE1}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqFilenamePE2,${filenamePrefix}${filenamePartSeperator}${filenameSuffixDiscardedReads}${filenamePartSeperator}${filenameSuffixPE2}${fastqExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilenameSR,${demultiplexedSampleFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedSampleFastqFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -compressedDemultiplexedDiscardedFastqFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${gzipExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -compressedDemultiplexedSampleFastqFilepathSR,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenameSR},,, -compressedDemultiplexedSampleFastqFilepathPE1,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE1},,, -compressedDemultiplexedSampleFastqFilepathPE2,${runResultsDir}/${compressedDemultiplexedSampleFastqFilenamePE2},,, -#,,,, -demultiplexedSampleFastqChecksumFilenameSR,${demultiplexedSampleFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE1,${demultiplexedSampleFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedSampleFastqChecksumFilenamePE2,${demultiplexedSampleFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenameSR,${demultiplexedDiscardedFastqFilenameSR}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE1,${demultiplexedDiscardedFastqFilenamePE1}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -demultiplexedDiscardedFastqChecksumFilenamePE2,${demultiplexedDiscardedFastqFilenamePE2}${md5sumExtension},use these for demultiplexed reads assigned to a sample,, -#,,,, -log,log.log,,, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow.csv deleted file mode 100644 index 599c863c59..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow.csv +++ /dev/null @@ -1,32 +0,0 @@ -name,protocol_name,PreviousSteps_name -Demultiplex,Demultiplex, -Zipfq,Zipfq,Demultiplex -Fastqc,Fastqc,Zipfq -BwaAlignLeft,BwaAlignLeft,Fastqc -BwaAlignRight,BwaAlignRight,Fastqc -BwaSampe,BwaSampe,"BwaAlignLeft, BwaAlignRight" -SamToBam,SamToBam,BwaSampe -SamSort,SamSort,SamToBam -PicardQC,PicardQC,SamSort -Markduplicates,Markduplicates,SamSort -RealignTargetCreator,RealignTargetCreator,Markduplicates -Realign,Realign,RealignTargetCreator -Fixmates,Fixmates,Realign -CovariatesBefore,CovariatesBefore,Fixmates -Recalibrate,Recalibrate,"Fixmates, CovariatesBefore" -SamSortRecal,SamSortRecal,Recalibrate -CovariatesAfter,CovariatesAfter,SamSortRecal -AnalyzeCovariates,AnalyzeCovariates,"CovariatesBefore, CovariatesAfter" -MergeBam,MergeBam,SamSortRecal -PicardQCrecal,PicardQCrecal,MergeBam -Coverage,Coverage,MergeBam -CoverageGATK,CoverageGATK,MergeBam -IndelGenotyper,IndelGenotyper,MergeBam -FilterIndels,FilterIndels,IndelGenotyper -UnifiedGenotyper,UnifiedGenotyper,MergeBam -MakeIndelMask,MakeIndelMask,FilterIndels -GenomicAnnotator,GenomicAnnotator,UnifiedGenotyper -VariantAnnotator,VariantAnnotator,GenomicAnnotator -VcfToTable,VcfToTable,VariantAnnotator -ConcordanceCheck,ConcordanceCheck,"MergeBam, UnifiedGenotyper" -QCReport,QCReport,"PicardQCrecal, Markduplicates, ConcordanceCheck, Coverage, VcfToTable" \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_ConcordanceQCReport.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_ConcordanceQCReport.csv deleted file mode 100644 index c3d84a46c6..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_ConcordanceQCReport.csv +++ /dev/null @@ -1,3 +0,0 @@ -name,protocol_name,PreviousSteps_name -ConcordanceCheck,ConcordanceCheck, -QCReport,QCReport,ConcordanceCheck \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_QCReport.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_QCReport.csv deleted file mode 100644 index 2a5d401881..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_QCReport.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -QCReport,QCReport, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_create_ngs_projects.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_create_ngs_projects.csv deleted file mode 100644 index 1c037734e1..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_create_ngs_projects.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -CreateInhouseProjects,CreateInhouseProjects, diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_data_archiving.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_data_archiving.csv deleted file mode 100644 index c023d32f9e..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_data_archiving.csv +++ /dev/null @@ -1,5 +0,0 @@ -name,protocol_name,PreviousSteps_name -RunGerald,RunGerald, -CopyFqToRawdatadir,CopyFqToRawdatadir,RunGerald -Demultiplex,Demultiplex,CopyFqToRawdatadir -CreateFinalReport,CreateFinalReport, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_demultiplex.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_demultiplex.csv deleted file mode 100644 index 8d29426647..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_demultiplex.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -Demultiplex,Demultiplex, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_realignmentAndSnpCalling.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_realignmentAndSnpCalling.csv deleted file mode 100644 index 278ce852a6..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_realignmentAndSnpCalling.csv +++ /dev/null @@ -1,31 +0,0 @@ -name,protocol_name,PreviousSteps_name -Fastqc,Fastqc, -BwaAlignLeft,BwaAlignLeft, -BwaAlignRight,BwaAlignRight, -BwaSampe,BwaSampe,"BwaAlignLeft, BwaAlignRight" -SamToBam,SamToBam,BwaSampe -SamSort,SamSort,SamToBam -PicardQC,PicardQC,SamSort -Markduplicates,Markduplicates,SamSort -RealignTargetCreator,RealignTargetCreator,Markduplicates -Realign,Realign,RealignTargetCreator -Fixmates,Fixmates,Realign -CovariatesBefore,CovariatesBefore,Fixmates -Recalibrate,Recalibrate,"Fixmates, CovariatesBefore" -SamSortRecal,SamSortRecal,Recalibrate -CovariatesAfter,CovariatesAfter,SamSortRecal -AnalyzeCovariates,AnalyzeCovariates,"CovariatesBefore, CovariatesAfter" -MergeBam,MergeBam,SamSortRecal -PicardQCrecal,PicardQCrecal,MergeBam -Coverage,Coverage,MergeBam -CoverageGATK,CoverageGATK,MergeBam -IndelGenotyper,IndelGenotyper,MergeBam -FilterIndels,FilterIndels,IndelGenotyper -UnifiedGenotyper,UnifiedGenotyper,MergeBam -MakeIndelMask,MakeIndelMask,FilterIndels -GenomicAnnotator,GenomicAnnotator,UnifiedGenotyper -VariantAnnotator,VariantAnnotator,GenomicAnnotator -VcfToTable,VcfToTable,VariantAnnotator -ConcordanceCheck,ConcordanceCheck,"MergeBam, UnifiedGenotyper" -QCReport,QCReport,"PicardQCrecal, Markduplicates, ConcordanceCheck, Coverage, VcfToTable" -CopyToResultsDir,CopyToResultsDir,"Fastqc, MergeBam, PicardQCrecal, VariantAnnotator, VcfToTable, ConcordanceCheck, QCReport" \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_realignmentAndSnpCallingNonHuman.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_realignmentAndSnpCallingNonHuman.csv deleted file mode 100644 index 0ffcf4762e..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_workflow_realignmentAndSnpCallingNonHuman.csv +++ /dev/null @@ -1,20 +0,0 @@ -name,protocol_name,PreviousSteps_name -Fastqc,Fastqc, -BwaAlignLeft,BwaAlignLeft,Fastqc -BwaAlignRight,BwaAlignRight,Fastqc -BwaSampe,BwaSampe,"BwaAlignLeft, BwaAlignRight" -SamToBam,SamToBam,BwaSampe -SamSort,SamSort,SamToBam -PicardQC,PicardQC,SamSort -Markduplicates,Markduplicates,SamSort -MergeBam,MergeBam,Markduplicates -Coverage,Coverage,MergeBam -CoverageGATK,CoverageGATK,MergeBam -IndelGenotyper,IndelGenotyper,MergeBam -FilterIndels,FilterIndels,IndelGenotyper -UnifiedGenotyper,UnifiedGenotyper,MergeBam -GenomicAnnotator,GenomicAnnotator,UnifiedGenotyper -MakeIndelMask,MakeIndelMask,UnifiedGenotyper -VariantFiltration,VariantFiltration,MakeIndelMask -VcfToTable,VcfToTable,VariantFiltration -QCReport,QCReport,"PicardQC, Markduplicates, Coverage, VcfToTable" \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_worksheet_test.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_worksheet_test.csv deleted file mode 100644 index a3472dec6f..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/in-house_worksheet_test.csv +++ /dev/null @@ -1,3 +0,0 @@ -laboratory Fee,internalSampleID,externalSampleID,project,validationLog,contact,labStatusPhase,labStatusComments,lastUpDate,sequencingStartDate,sequencer,run,flowcell,lane,barcodeGAF,barcode,seqType,prepKit,capturingKit,arrayFile,arrayID,GAF_QC_Name,GAF_QC_Date,GAF_QC_Status,GCC_Analysis,GCC_QC_Name,GCC_QC_Date,GCC_QC_Status,Data_Responsibility,TargetDateShipment,DataShippedDate,DataShippedTo,DataShippedBy,Comments -,587,testSample,testProject,*Bad GCC_QC_Status*,Agata Szperl ,Finished Successfully,"same as 11, DO NOT MERGE",1/9/12,111202,SN163,0448TestSubset,AC0A5UACXX,7,GAF 06 CAACCT,CAACCT,PE,NEB,SureSelect_All_Exon_50MB,GenomeStudio01122011,66,Pieter,20111212,Passed,Yes,,,,,,,,, -,588,testSample,testProject,*Bad GCC_QC_Status*,Agata Szperl ,Finished Successfully,,1/9/12,111202,SN163,0448TestSubset,AC0A5UACXX,7,GAF 12 GGAACT,GGAACT,PE,NEB,SureSelect_All_Exon_50MB,GenomeStudio01122011,66,Pieter,20111212,Passed,Yes,,,,,,,,, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/lifelines_pilot1_gwas_parameters.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/lifelines_pilot1_gwas_parameters.csv deleted file mode 100644 index 43ffc528ff..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/lifelines_pilot1_gwas_parameters.csv +++ /dev/null @@ -1,21 +0,0 @@ -Name,defaultValue,description,dataType,hasOne_name -plinkFileNameRaw,,name of plink file within raw data directory hence without extension and without path,, -familyIDsFileName,,"name of txt file with four columns: FamID, SampleID, FatherID and MotherID",, -parentIDsFileName,,,, -removeIDsFileName,,,, -projectDir,/target/gpfs2/gcc/groups/gcc/lifelines_pilot1/,,, -projectRawDataDir,{$projectDir}/rawdata/,,, -projectJobsDir,{$projectDir}/jobs/,,, -projectLogsDir,{$projectDir}/logs/,,, -projectIntermediateDir,{$projectDir}/intermediate/,,, -projectResultsDir,{$projectDir}/results/,,, -toolDir,/target/gpfs2/gcc/tools/,,, -plink,${toolDir}/plink-1.07-x86_64/plink-1.07-x86_64/plink,,, -plinkFileRaw,${projectRawDataDir}/${plinkFileNameRaw},,, -familyIDsFile,${projectRawDataDir}/${familyIDsFileName},,, -parentIDsFile,${projectRawDataDir}/${parentIDsFileName},,, -removeIDsFile,${projectRawDataDir}/${removeIDsFileName},,, -plinkFileFixedFamilies,${projectIntermediateDir}/${plinkFileRaw}_fixed_families,,, -plinkFileFixedParents,${projectIntermediateDir}/${plinkFileRaw}_fixed_parents,,, -plinkFileClean,${projectIntermediateDir}/${plinkFileRaw}_clean,,, -log,log.log,,, \ No newline at end of file diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/lifelines_pilot1_gwas_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/lifelines_pilot1_gwas_workflow.csv deleted file mode 100644 index 49681fe163..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/lifelines_pilot1_gwas_workflow.csv +++ /dev/null @@ -1,2 +0,0 @@ -name,protocol_name,PreviousSteps_name -FixColumns,FixColumns, diff --git a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/ngs_demo_workflow.csv b/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/ngs_demo_workflow.csv deleted file mode 100644 index 06e56ebe3a..0000000000 --- a/modules/compute/demo/run0482/compute2/molgenis_compute-f6e477a/workflows/ngs_demo_workflow.csv +++ /dev/null @@ -1,8 +0,0 @@ -name,protocol_name,PreviousSteps_name -Fastqc,Fastqc, -BwaAlignLeft,BwaAlignLeft,Fastqc -BwaAlignRight,BwaAlignRight,Fastqc -BwaSampe,BwaSampe,"BwaAlignLeft, BwaAlignRight" -SamToBam,SamToBam,BwaSampe -SamSort,SamSort,SamToBam -PicardQC,PicardQC,SamSort diff --git a/modules/compute/demo/run0482/run0482.csv b/modules/compute/demo/run0482/run0482.csv deleted file mode 100644 index 08beb6c36a..0000000000 --- a/modules/compute/demo/run0482/run0482.csv +++ /dev/null @@ -1,44 +0,0 @@ -0,internalSampleID,externalSampleID,project,contact,validationLog,labStatusPhase,labStatusComments,lastUpDate,sequencingStartDate,sequencer,run,flowcell,lane,barcodeMenu,seqType,prepKit,capturingKit,arrayFile,arrayID,GAF_QC_Name,GAF_QC_Date,GAF_QC_Status,GCC_Analysis,GCC_QC_Name,GCC_QC_Date,GCC_QC_Status,TargetDateShipment,DataShippedDate,DataShippedTo,DataShippedBy,Comments,barcode,barcodeType -,1208,2048,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 02 CGATGT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CGATGT,RPI -,1209,2049,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 03 TTAGGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,TTAGGC,RPI -,1210,2050,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 04 TGACCA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,TGACCA,RPI -,1211,2051,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 05 ACAGTG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACAGTG,RPI -,1212,2055,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 09 GATCAG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GATCAG,RPI -,1213,Serum_0102,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 33 CAGGCG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAGGCG,RPI -,1214,CSF_473,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 27 ATTCCT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATTCCT,RPI -,1215,H2O,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 1",,121113,SN163,0482,BC1B32ACXX,1,RPI 06 GCCAAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GCCAAT,RPI -,1216,2047,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 01 ATCACG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATCACG,RPI -,1217,2052,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 06 GCCAAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GCCAAT,RPI -,1218,2053,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 07 CAGATC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAGATC,RPI -,1219,2054,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 08 ACTTGA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACTTGA,RPI -,1220,2056,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 10 TAGCTT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,TAGCTT,RPI -,1221,Serum_0103,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 34 CATGGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CATGGC,RPI -,1222,Granulocytes,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 31 CACGAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CACGAT,RPI -,1223,H2O,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 2",,121113,SN163,0482,BC1B32ACXX,2,RPI 11 GGCTAC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GGCTAC,RPI -,1224,T07_16098,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 13 AGTCAA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,AGTCAA,RPI -,1225,T07_17332,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 14 AGTTCC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,AGTTCC,RPI -,1226,T08_0617,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 15 ATGTCA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATGTCA,RPI -,1227,T06_16822,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 16 CCGTCC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CCGTCC,RPI -,1228,T06_0601,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 3",,121113,SN163,0482,BC1B32ACXX,3,RPI 17 GTAGAG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTAGAG,RPI -,1229,T03_62818,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 18 GTCCGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTCCGC,RPI -,1230,T02_104821,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 19 GTGAAA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTGAAA,RPI -,1231,T97_13615,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 20 GTGGCC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTGGCC,RPI -,1232,T10_18095,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 21 GTTTCG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GTTTCG,RPI -,1233,T09_20721,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 4",,121113,SN163,0482,BC1B32ACXX,4,RPI 22 CGTACG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CGTACG,RPI -,1234,T09_04104,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 23 GAGTGG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GAGTGG,RPI -,1235,T09_15160,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 24 GGTAGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,GGTAGC,RPI -,1236,T08_15966,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 25 ACTGAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACTGAT,RPI -,1237,T05_15373,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 26 ATGAGC,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATGAGC,RPI -,1238,T07_17380,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 5",,121113,SN163,0482,BC1B32ACXX,5,RPI 27 ATTCCT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ATTCCT,RPI -,1239,T09_15289,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 28 CAAAAG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAAAAG,RPI -,1240,T06_10848,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 29 CAACTA,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CAACTA,RPI -,1241,T02_01220,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 30 CACCGG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CACCGG,RPI -,1242,n_CD4,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 31 CACGAT,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,CACGAT,RPI -,1243,Granulocytes,RNAseqSebo,Sebo Withof ,*Bad GCC_QC_Status*,Finished Successfully,"50 bp run, pool 6",,121113,SN163,0482,BC1B32ACXX,6,RPI 05 ACAGTG,SR,SmallRNA,None,,,Pieter,20121116,Failed,No,,,,,,,,,ACAGTG,RPI -,1279,ctr2_tRNA_0h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 973, 50 bp run, pool 14",,121113,SN163,0482,BC1B32ACXX,7,RPI 07 CAGATC,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,CAGATC,RPI -,1280,ctr4_RPF_0h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 974, 50 bp run, pool 14",,121113,SN163,0482,BC1B32ACXX,7,RPI 10 TAGCTT,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,TAGCTT,RPI -,1281,uc1_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 975, 50 bp run, pool 14",,121113,SN163,0482,BC1B32ACXX,7,RPI 21 GTTTCG,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,GTTTCG,RPI -,1282,ctr2_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 953, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 09 GATCAG,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,GATCAG,RPI -,1283,ctr4_tRNA_2h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 954, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 08 ACTTGA,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,ACTTGA,RPI -,1284,ctr5_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 955, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 21 GTTTCG,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,GTTTCG,RPI -,1285,UC2_tRNA_24h,RibosomeSeq,Cleo van Diemen ,*Bad GCC_QC_Status*,Finished Successfully,"herhaling sample 956, 50 bp run, pool 8",,121113,SN163,0482,BC1B32ACXX,8,RPI 15 ATGTCA,SR,SmallRNA,None,,,Pieter,20120920,Failed,No,,,,,,,,,ATGTCA,RPI \ No newline at end of file diff --git a/status.txt b/status.txt new file mode 100644 index 0000000000..e0c7c0dbd7 --- /dev/null +++ b/status.txt @@ -0,0 +1,3822 @@ +# On branch master +# Changes to be committed: +# (use "git reset HEAD ..." to unstage) +# +# new file: modules/compute/demo/asobara/parameters.csv +# new file: modules/compute/demo/asobara/protocols/Abyss.ftl +# new file: modules/compute/demo/asobara/protocols/Fastqc.ftl +# new file: modules/compute/demo/asobara/protocols/Submit.sh.ftl +# new file: modules/compute/demo/asobara/templates/Helpers.ftl +# new file: modules/compute/demo/asobara/templates/Macros.ftl +# new file: modules/compute/demo/asobara/workflow.csv +# new file: modules/compute/demo/asobara/worksheet.csv +# new file: modules/compute/demo/burnDown/output/dataTransfer.sh +# new file: modules/compute/demo/burnDown/output/parameters.csv +# new file: modules/compute/demo/burnDown/output/runlocal.sh +# new file: modules/compute/demo/burnDown/output/s00_CreateChartPDF_64.sh +# new file: modules/compute/demo/burnDown/output/submit.sh +# new file: modules/compute/demo/burnDown/output/workflow.csv +# new file: modules/compute/demo/burnDown/output/worksheet.csv +# new file: modules/compute/demo/burnDown/parameters.csv +# new file: modules/compute/demo/burnDown/protocols/CreateChartPDF.ftl +# new file: modules/compute/demo/burnDown/protocols/DataTransfer.sh.ftl +# new file: modules/compute/demo/burnDown/protocols/Submit.sh.ftl +# new file: modules/compute/demo/burnDown/templates/Footer.ftl +# new file: modules/compute/demo/burnDown/templates/Header.ftl +# new file: modules/compute/demo/burnDown/workflow.csv +# new file: modules/compute/demo/burnDown/worksheet.csv +# new file: modules/compute/demo/debug/protocols/Submit.sh.ftl +# new file: modules/compute/demo/debugCompute4/assembly.zip +# new file: modules/compute/demo/debugCompute4/assembly/Asobara_worksheet_run0486.csv +# new file: modules/compute/demo/debugCompute4/assembly/Asobara_worksheet_run0486_noInternalSampleID.csv +# new file: modules/compute/demo/debugCompute4/assembly/example_cmd.sh +# new file: modules/compute/demo/debugCompute4/assembly/parameters.csv +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Abyss.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Fastqc.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Footer.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Header.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Helpers.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Macros.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/NGSHeader.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/PBSHeader.ftl +# new file: modules/compute/demo/debugCompute4/assembly/protocols/Submit.sh.ftl +# new file: modules/compute/demo/debugCompute4/assembly/scripts/Asobara_worksheet_run0486_noInternalSampleID.csv +# new file: modules/compute/demo/debugCompute4/assembly/scripts/dataTransfer.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/parameters.csv +# new file: modules/compute/demo/debugCompute4/assembly/scripts/runlocal.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_1.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_10.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_11.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_12.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_13.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_14.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_15.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_16.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_17.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_18.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_19.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_2.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_20.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_21.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_22.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_23.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_24.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_25.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_26.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_27.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_28.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_29.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_3.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_30.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_31.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_32.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_33.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_34.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_35.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_36.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_37.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_38.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_39.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_4.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_40.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_5.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_6.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_7.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_8.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s00_FastQC_9.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_73_AM1_73.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_75_AM1_75.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_77_AM1_77.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_79_AM1_79.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_AM1_81_AM1_81.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_73_KG1_73.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_75_KG1_75.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_77_KG1_77.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_79_KG1_79.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/s01_AbySS_Asobara_Japonica_KG1_81_KG1_81.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/submit.sh +# new file: modules/compute/demo/debugCompute4/assembly/scripts/workflow.csv +# new file: modules/compute/demo/debugCompute4/assembly/system +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-cluster.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-download-grid.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-errorfile.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-exe-grid-dir.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-exe-grid.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-extrafile.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-jdl-grid.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-logfile.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-outfile.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-submit.ftl +# new file: modules/compute/demo/debugCompute4/assembly/templates_/templ-upload-grid.ftl +# new file: modules/compute/demo/debugCompute4/assembly/workflow.csv +# new file: modules/compute/demo/debugCompute4/output/parameters.csv +# new file: modules/compute/demo/debugCompute4/output/runlocal.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_1.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_10.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_11.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_12.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_13.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_14.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_15.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_16.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_17.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_18.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_19.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_2.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_20.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_21.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_22.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_23.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_24.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_25.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_26.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_27.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_28.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_29.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_3.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_30.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_31.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_32.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_33.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_34.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_35.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_36.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_37.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_38.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_39.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_4.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_40.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_5.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_6.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_7.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_8.sh +# new file: modules/compute/demo/debugCompute4/output/s00_FastQC_9.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_73_AM1_73.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_75_AM1_75.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_77_AM1_77.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_79_AM1_79.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_AM1_81_AM1_81.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_73_KG1_73.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_75_KG1_75.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_77_KG1_77.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_79_KG1_79.sh +# new file: modules/compute/demo/debugCompute4/output/s01_AbySS_Asobara_Japonica_KG1_81_KG1_81.sh +# new file: modules/compute/demo/debugCompute4/output/submit.sh +# new file: modules/compute/demo/debugCompute4/output/workflow.csv +# new file: modules/compute/demo/debugCompute4/output/worksheet.csv +# new file: modules/compute/demo/debugCompute4/parameters.csv +# new file: modules/compute/demo/debugCompute4/protocols/Abyss.ftl +# new file: modules/compute/demo/debugCompute4/protocols/Fastqc.ftl +# new file: modules/compute/demo/debugCompute4/protocols/Footer.ftl +# new file: modules/compute/demo/debugCompute4/protocols/Header.ftl +# new file: modules/compute/demo/debugCompute4/protocols/Helpers.ftl +# new file: modules/compute/demo/debugCompute4/protocols/Macros.ftl +# new file: modules/compute/demo/debugCompute4/protocols/NGSHeader.ftl +# new file: modules/compute/demo/debugCompute4/protocols/PBSHeader.ftl +# new file: modules/compute/demo/debugCompute4/protocols/Submit.sh.ftl +# new file: modules/compute/demo/debugCompute4/workflow.csv +# new file: modules/compute/demo/debugCompute4/worksheet.csv +# new file: modules/compute/demo/debugFolding/inputdir/workflow_QCReport.csv +# new file: modules/compute/demo/demoWorkflow/parameters.csv +# new file: modules/compute/demo/demoWorkflow/protocols/BwaAlignLeft.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/BwaAlignRight.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/BwaSampe.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Covariates.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/CovariatesAfter.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/CovariatesBefore.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Coverage.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/CreateInhouseProjects.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/DataTransfer.sh.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/DeployDbsnpIndelResources.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Fixmates.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/GenerateReference.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/GenomicAnnotator.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Helpers.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/IndexReference.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Initialize.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/InstallTools.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/InstallWget.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Markduplicates.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/MergeBam.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/PicardQC.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/PicardQCrecal.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/QCReport.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/QCReportTemplate.tex +# new file: modules/compute/demo/demoWorkflow/protocols/Realign.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/RealignTargetCreator.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Recalibrate.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/SamSort.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/SamSortRecal.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/SamToBam.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/Submit.sh.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/UnifiedGenotyper.ftl +# new file: modules/compute/demo/demoWorkflow/protocols/VariantAnnotator.ftl +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/dedupmetrics.txt +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.aux +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.log +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.tex +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCReport.toc +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_QCStatistics.csv +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_qcstatisticsdescription.tex +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_qcstatisticstable.tex +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectName_workflow.png +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/qc/projectbaitset.txt +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq.gz +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq.md5 +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_2.fq.gz +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/projects/projectName/run00/rawdata/ngs/20130129_simMachine_0001_FLOWCELL_L1_None_2.fq.md5 +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/rawdata/ngs/20130129_simMachine_0001_FLOWCELL/20130129_simMachine_0001_FLOWCELL_L1_1.fq.gz +# new file: modules/compute/demo/demoWorkflow/root/groups/gaf/rawdata/ngs/20130129_simMachine_0001_FLOWCELL/20130129_simMachine_0001_FLOWCELL_L1_2.fq.gz +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbSNP135.tabdelim.table +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbSNP135.tabdelim.table.idx +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbsnp_129_b37_human_g1k_v37.rod +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/dbsnp/dbsnp_129_b37_human_g1k_v37.rod.idx +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indels/1kg_pilot_release_merged_indels_sites_hg19_human_g1k_v37.vcf +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indels/1kg_pilot_release_merged_indels_sites_hg19_human_g1k_v37.vcf.idx +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.dict +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.amb +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.ann +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.bwt +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.fai +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.pac +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.rbwt +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.rpac +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.rsa +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/simulatedReferenceGenome.fa.sa +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/indices/visualization.txt +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/#simulated_baits.interval_list# +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_baits.interval_list +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_baits_hg19_simulatedReferenceGenome.bed +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_targets.interval_list +# new file: modules/compute/demo/demoWorkflow/root/resources/hg19/intervals/simulated_targets_hg19_simulatedReferenceGenome.bed +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/Aligner.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/CountRecords.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/IndexToTable.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/StingUtils.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/activation-1.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/annotations-1.3.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/aopalliance-1.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/bcel-5.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/bsh-2.0b4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/colt-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-email-1.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-io-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-jexl-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-lang-2.5.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/commons-logging-1.1.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/concurrent-1.3.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/dom4j-1.6.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/google-collections-1.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/gson-1.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/guice-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jakarta-regexp-1.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/javassist-3.7.ga.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/javassist-3.8.0.GA.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jcommander-1.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jgrapht-jdk1.5-0.7.3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jna-3.2.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/jsr305-1.3.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/junit-3.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/lucene-core-3.0.3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/mail-1.4.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/picard-1.37.686.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/picard-private-parts-1702.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/reflections-0.9.5-RC2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/sam-1.37.686.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/scala-compiler-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/scala-library-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/simple-xml-2.0.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/slf4j-api-1.5.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/snakeyaml-1.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/stax-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/stax-api-1.0.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/testng-5.14.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/testng-5.5-jdk15.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/tribble-0.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.0.5069/Sting/dist/xml-apis-1.0.b2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/LICENSE +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/build.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/Aligner.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/AnalyzeCovariates.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/GenomeAnalysisTK.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/StingUtils.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/activation-1.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/asm-all-3.3.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/bcel-5.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/cofoja-1.0-20110609.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/colt-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-codec-1.5.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-email-1.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-httpclient-3.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-io-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-jexl-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-lang-2.5.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-logging-1.1.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/commons-math-2.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/concurrent-1.3.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/dom4j-1.6.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/drmaa-6.2u5p2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/freemarker-2.3.18.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/google-collections-1.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/gson-1.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jakarta-regexp-1.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/java-xmlbuilder-0.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/javassist-3.7.ga.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/javassist-3.8.0.GA.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jets3t-0.8.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jgrapht-jdk1.5-0.7.3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/jna-3.2.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/lucene-core-3.0.3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/mail-1.4.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/picard-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/picard-private-parts-2068.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/poi-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/poi-ooxml-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/poi-ooxml-schemas-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/reflections-0.9.5-RC2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/sam-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/scala-compiler-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/scala-library-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/simple-xml-2.0.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/slf4j-api-1.5.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/snakeyaml-1.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/snpeff-2.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/stax-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/stax-api-1.0.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/tribble-40.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/vcf.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/xml-apis-1.0.b2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/dist/xmlbeans-2.3.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/INDEX +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/Rd.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/data.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/hsearch.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/links.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/Meta/package.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/NAMESPACE +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/INDEX +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/Rd.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/data.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/hsearch.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/links.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/package.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/NAMESPACE +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/R/gsalib +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/R/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/R/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/AnIndex +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/aliases.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/paths.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/html/00Index.html +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/gsalib/html/R.css +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/help/AnIndex +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/help/aliases.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/help/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/help/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/help/paths.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/html/00Index.html +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib/html/R.css +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/gsalib_1.0.tar.gz +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/ivy.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/activation-1.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/asm-all-3.3.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/bcel-5.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/cofoja-1.0-20110609.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/colt-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-codec-1.5.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-email-1.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-httpclient-3.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-io-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-jexl-2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-lang-2.5.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-logging-1.1.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/commons-math-2.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/concurrent-1.3.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/dom4j-1.6.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/drmaa-6.2u5p2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/freemarker-2.3.18.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/google-collections-1.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/gson-1.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/jakarta-regexp-1.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/java-xmlbuilder-0.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/javassist-3.7.ga.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/javassist-3.8.0.GA.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/jets3t-0.8.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/jgrapht-jdk1.5-0.7.3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/jna-3.2.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/lucene-core-3.0.3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/mail-1.4.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/picard-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/picard-private-parts-2068.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/poi-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/poi-ooxml-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/poi-ooxml-schemas-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/reflections-0.9.5-RC2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/sam-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/scala-compiler-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/scala-library-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/simple-xml-2.0.4.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/slf4j-api-1.5.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/snakeyaml-1.7.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/snpeff-2.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/stax-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/stax-api-1.0.1.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/tribble-40.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/xml-apis-1.0.b2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/lib/xmlbeans-2.3.0.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/R.css +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/INDEX +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/Rd.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/data.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/hsearch.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/links.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/package.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/R/gsalib +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/R/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/R/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/AnIndex +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/aliases.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/paths.rds +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib/html/00Index.html +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/gsalib_1.0.tar.gz +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib_1.0.tar.gz +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/R/titvFPEst.R +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/SeparateQltout.cc +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/build_linux.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/build_mac.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/bwa_gateway.cpp +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/bwa_gateway.h +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/libenvironhack/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/libenvironhack/libenvironhack.c +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/c/libenvironhack/libenvironhack.dylib +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/b36tob37.chain +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/b37tob36.chain +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/b37tohg18.chain +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/b37tohg19.chain +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/hg18tob37.chain +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/hg19toHg18.chain +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/chainFiles/makeChains.py +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/doc/Ant_Help.tex +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/doc/GATK_Coding_Standards.pdf +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/doc/GATK_Coding_Standards.tex +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/doc/README +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKBAMFileSpan.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKBin.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKBinList.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKChunk.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/Aligner.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/Alignment.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWAPath.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Advanced.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Argument.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSite.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ClassType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Gather.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Gatherer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Hidden.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Input.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Output.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Tags.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/DownsampleType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/DownsamplingMethod.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMIndexContent.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMOverlap.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReaderBin.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/MicroSchedulerMBean.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/Storage.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/IterableIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Affection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Gender.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/PedigreeValidationType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Attribution.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Downsample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplex.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplexer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionBy.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RMD.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Reference.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RodWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypePriors.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Dinuc.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatum.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/StateKey.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/TableType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/clibrary/JNAUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobInfo.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobTemplate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionFactory.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaa.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/QueueVersion.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/AminoAcid.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/AminoAcidTable.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/ContigComparator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/HasGenomeLocation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/PathUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutorException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/Utils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/analysis/AminoAcid.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/analysis/AminoAcidTable.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/analysis/AminoAcidUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/IndexingVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/Pair.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/PrimitivePair.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/duplicates/DuplicateComp.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/DynamicClassResolutionException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/StingException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fasta/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/file/FileSystemInabilityToLockException.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentCollection.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureObject.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/IntervalMergingRule.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/IntervalSetRule.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/FileExtension.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/HardThresholdingOutputStream.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/Resource.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementFilter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup2/Notes +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/CapturedStreamOutput.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/InputStreamSettings.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/OutputStreamSettings.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/ProcessController.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/ProcessOutput.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/ProcessSettings.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/RuntimeUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/StreamLocation.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/StreamOutput.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/threading/ThreadPoolMonitor.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/threading/package-info.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleHeader.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/yaml/FieldOrderComparator.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/yaml/StingYamlRepresenter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/yaml/YamlUtils.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/net/sf/samtools/GATKChunkUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/BaseTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/MD5DB.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/StingTextReporter.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/WalkerTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/ArgumentMatchSiteUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/ArgumentMatchSourceUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/MockLocusShard.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMBAMDataSourceUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/executive/ReduceTreeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/clibrary/LibCUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/R/RScriptLibraryUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/ReservoirDownsamplerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/SimpleTimerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/runtime/ProcessControllerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/runtime/RuntimeUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/text/TextFormattingUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/threading/ThreadPoolMonitorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/Aligner.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/AnalyzeCovariates.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/CreatePackager.xsl +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/GATK-Picard.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/GATKEngine.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/GenomeAnalysisTK.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/PicardPrivate.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/packages/Queue.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/perl/liftOverVCF.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/perl/sortByRef.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QException.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QScript.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/JobRunInfo.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/JobRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/MappingEdge.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QEdge.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QNode.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/RunnerStatus.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/AutoIndexGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/IntersectIntervals.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/RetryException.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/HiSeq.10000.bgzip.vcf.gz +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/HiSeq.10000.vcf +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/HiSeq.10000.vcf.gz +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/TabularDataTest.dat +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/TabularDataTest2.dat +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/ValidatingPileupTargets.list +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/ceutrio.ped +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/defaultGATKConfig.cfg +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/diffTestMaster.vcf +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/diffTestTest.vcf +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.bam +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.bam.bai +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.simple.bai +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.simple.bam +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleFASTA.dict +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleFASTA.fasta +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleFASTA.fasta.fai +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleNORG.bam +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/exampleNORG.bam.bai +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/gFFTest.gff +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/recalConfig_1KG.cfg +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/sampleBedFile.bed +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/small.dbsnp.rod +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/tranches.4.txt +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/tranches.6.txt +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/tranches.raw.dat +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/vcf/vcfWithGenotypes.vcf +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/public/testdata/vcf/vcfWithoutGenotypes.vcf +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/helpTemplates/common.html +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/helpTemplates/generic.index.template.html +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/helpTemplates/generic.template.html +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/helpTemplates/style.css +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/ivysettings.properties +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/ivysettings.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/edu.mit.broad/picard-private-parts-2068.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/edu.mit.broad/picard-private-parts-2068.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/gov.nist/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/gov.nist/Jama-1.0.2.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.snpeff/snpeff-2.0.2.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.snpeff/snpeff-2.0.2.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/picard-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/picard-1.55.985.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/sam-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/sam-1.55.985.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/org.broad/tribble-40.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/GATK-1.3-24-gc8b1c92/settings/repository/org.broad/tribble-40.xml +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bntseq.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwape.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwase.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwaseqio.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwt.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwt_lite.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtaln.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtgap.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtindex.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtio.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtmisc.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtsw2_aux.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtsw2_chain.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtsw2_core.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/bwtsw2_main.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/cs2nt.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/is.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/kstring.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/main.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/simple_dp.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/stdaln.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/.deps/utils.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/AUTHORS +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/BWA_read_group_patch.diff +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/COPYING +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/ChangeLog +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/INSTALL +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/Makefile.am +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/Makefile.in +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/NEWS +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/README +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/aclocal.m4 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/autogen.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/autom4te.cache/output.0 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/autom4te.cache/output.1 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/autom4te.cache/requests +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/autom4te.cache/traces.0 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/autom4te.cache/traces.1 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bntseq.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bntseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwa +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwa.1 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwape.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwase.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwase.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwaseqio.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/.deps/QSufSort.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/.deps/bwt_gen.Po +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/Makefile.am +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/Makefile.in +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/QSufSort.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/QSufSort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/bwt_gen.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/bwt_gen.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_gen/libbwtgen.a +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_lite.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwt_lite.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtgap.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtgap.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtindex.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtio.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtmisc.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtsw2.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtsw2_aux.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtsw2_chain.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtsw2_core.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/bwtsw2_main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/cleanup.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/config.guess +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/config.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/config.h.in +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/config.log +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/config.status +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/config.sub +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/configure +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/configure.in +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/cs2nt.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/depcomp +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/install-sh +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/is.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/khash.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/kseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/ksort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/kstring.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/kstring.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/kvec.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/libbwacore.a +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/m4/acx_pthread.m4 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/main.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/missing +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/out.sai +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/qualfa2fq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/simple_dp.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/solid2fastq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/sracsfq2fq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/stamp-h1 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/stdaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/stdaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/utils.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.8c_patched/utils.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9.tar.bz2 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/COPYING +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/ChangeLog +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/NEWS +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/README +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bamlite.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bamlite.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bntseq.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bntseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwa +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwa.1 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwa.txt +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwape.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwase.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwase.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwaseqio.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/QSufSort.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/QSufSort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/bwa.txt +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/bwt_gen.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/bwt_gen.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_gen/libbwtgen.a +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_lite.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwt_lite.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtgap.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtgap.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtindex.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtio.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtmisc.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtsw2.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtsw2_aux.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtsw2_chain.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtsw2_core.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/bwtsw2_main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/cs2nt.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/is.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/khash.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/kseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/ksort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/kstring.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/kstring.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/kvec.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/main.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/out.sai +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/qualfa2fq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/simple_dp.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/solid2fastq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/stdaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/stdaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/utils.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.5.9/utils.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2.tar.bz2 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/COPYING +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/ChangeLog +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/NEWS +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/QSufSort.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/QSufSort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/README +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bamlite.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bamlite.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bntseq.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bntseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwa +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwa.1 +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwa.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwa.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwape.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwase.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwase.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwaseqio.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwt.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwt.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwt_gen.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwt_lite.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwt_lite.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtgap.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtgap.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtindex.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtio.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtmisc.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtsw2.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtsw2_aux.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtsw2_chain.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtsw2_core.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtsw2_main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/bwtsw2_pair.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/cs2nt.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/fastmap.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/is.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/khash.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/kseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/ksort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/kstring.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/kstring.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/ksw.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/ksw.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/kvec.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/libbwa.a +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/main.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/qualfa2fq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/simple_dp.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/solid2fastq.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/stdaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/stdaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/utils.c +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/utils.h +# new file: modules/compute/demo/demoWorkflow/root/tools/bwa-0.6.2/xa2multi.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/createInsertSizePlot/createInsertSizePlot.R +# new file: modules/compute/demo/demoWorkflow/root/tools/getStatistics_20121127/.Rapp.history +# new file: modules/compute/demo/demoWorkflow/root/tools/getStatistics_20121127/NiceColumnNames.csv +# new file: modules/compute/demo/demoWorkflow/root/tools/getStatistics_20121127/getStatistics.R +# new file: modules/compute/demo/demoWorkflow/root/tools/getStatistics_20121127/getStatisticsFunctions.R +# new file: modules/compute/demo/demoWorkflow/root/tools/getStatistics_20121127/getStatisticsReadCommandLineArgs.R +# new file: modules/compute/demo/demoWorkflow/root/tools/getTools.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61.tgz +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/AddOrReplaceReadGroups.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/BamIndexStats.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/BamToBfq.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/BuildBamIndex.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CalculateHsMetrics.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CleanSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CollectAlignmentSummaryMetrics.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CollectGcBiasMetrics.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CollectInsertSizeMetrics.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CollectMultipleMetrics.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CollectRnaSeqMetrics.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CompareSAMs.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/CreateSequenceDictionary.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/DownsampleSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/EstimateLibraryComplexity.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/ExtractIlluminaBarcodes.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/ExtractSequences.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/FastqToSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/FilterSamReads.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/FixMateInformation.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/IlluminaBasecallsToSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/IntervalListTools.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/MarkDuplicates.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/MeanQualityByCycle.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/MergeBamAlignment.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/MergeSamFiles.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/NormalizeFasta.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/QualityScoreDistribution.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/ReorderSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/ReplaceSamHeader.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/RevertSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/SamFormatConverter.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/SamToFastq.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/SortSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/ValidateSamFile.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/ViewSam.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/picard-1.61.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/picard-tools-1.61/sam-1.61.jar +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/AUTHORS +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/COPYING +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/ChangeLog +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/INSTALL +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/Makefile.mingw +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/NEWS +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam2bcf.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam2bcf.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam2bcf_indel.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam2depth.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_aux.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_cat.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_color.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_endian.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_import.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_index.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_lpileup.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_mate.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_md.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_pileup.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_plcmd.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_reheader.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_rmdup.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_rmdupse.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_sort.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_stat.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bam_tview.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bamtk.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/README +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/bcf.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/bcf.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/bcf.tex +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/bcf2qcall.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/bcftools +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/bcfutils.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/call1.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/em.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/fet.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/index.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/kfunc.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/kmin.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/kmin.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/libbcf.a +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/main.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/mut.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/prob1.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/prob1.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/vcf.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bcftools/vcfutils.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bedidx.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bgzf.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bgzf.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bgzip.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/blast2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/bowtie2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/cut_target.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/errmod.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/errmod.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/00README.txt +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/bam2bed.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/calDepth.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/ex1.fa +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/ex1.sam.gz +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/toy.fa +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/examples/toy.sam +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/export2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/faidx.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/faidx.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/interpolate_sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/khash.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/klist.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/knetfile.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/knetfile.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kprobaln.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kprobaln.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kseq.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/ksort.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kstring.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/kstring.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/libbam.a +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/maq2sam-long +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/maq2sam-short +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/md5fa +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/md5sum-lite +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/HmmGlocal.java +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/Makefile +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/blast2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/bowtie2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/export2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/interpolate_sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam-long +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam-long.dSYM/Contents/Info.plist +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam-long.dSYM/Contents/Resources/DWARF/maq2sam-long +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam-short +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam-short.dSYM/Contents/Info.plist +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam-short.dSYM/Contents/Resources/DWARF/maq2sam-short +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/maq2sam.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/md5.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/md5.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/md5fa +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/md5fa.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/md5sum-lite +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/novo2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/psl2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/sam2vcf.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/samtools.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/seqtk +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/seqtk.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/soap2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/varfilter.py +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/wgsim +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/wgsim.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/wgsim_eval.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/misc/zoom2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/novo2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/phase.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/psl2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/razf.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/razf.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/razip.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sam.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sam.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sam2vcf.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sam_header.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sam_header.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sam_view.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sample.c +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/sample.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/samtools +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/samtools.1 +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/samtools.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/seqtk +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/soap2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/varfilter.py +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/vcfutils.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/wgsim +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/wgsim_eval.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/win32/xcurses.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/win32/zconf.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/win32/zlib.h +# new file: modules/compute/demo/demoWorkflow/root/tools/samtools-0.1.18/zoom2sam.pl +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/createDedupTableFunctions.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/createSNPTable_19mar2012/createSNPTable.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/createSNPTable_19mar2012/createSNPTable.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/createSNPTable_19mar2012/createSNPTableFunctions.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/createSNPTable_19mar2012/readCommandLineArgs.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/createDedupTableFunctions.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/getDedupInfo.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/getDedupInfo.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/out.tex +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/readCommandLineArgs.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/run.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/testdata/110303_SN163_0393_A80MP0ABXX_L4_AGAGAT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/testdata/110303_SN163_0393_A80MP0ABXX_L4_TAATTT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/testdata/111018_SN163_0434_AD0AP0ACXX_L5_AGAGAT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/testdata/111018_SN163_0434_AD0AP0ACXX_L5_TAATTT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/getDedupInfo_23mar2012/testdata/getdata.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/import.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/out.tex +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/readCommandLineArgs.R +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/run.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/testdata/110303_SN163_0393_A80MP0ABXX_L4_AGAGAT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/testdata/110303_SN163_0393_A80MP0ABXX_L4_TAATTT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/testdata/111018_SN163_0434_AD0AP0ACXX_L5_AGAGAT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/testdata/111018_SN163_0434_AD0AP0ACXX_L5_TAATTT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/testdata/getdata.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/scripts/transferData.sh +# new file: modules/compute/demo/demoWorkflow/root/tools/snpEff_2_0_5/snpEff.config +# new file: modules/compute/demo/demoWorkflow/root/tools/snpEff_2_0_5/snpEff.jar +# new file: modules/compute/demo/demoWorkflow/run00/dataTransfer.sh +# new file: modules/compute/demo/demoWorkflow/run00/hoi +# new file: modules/compute/demo/demoWorkflow/run00/parameters.csv +# new file: modules/compute/demo/demoWorkflow/run00/runlocal.sh +# new file: modules/compute/demo/demoWorkflow/run00/s00_Initialize_projectName.sh +# new file: modules/compute/demo/demoWorkflow/run00/s01_BwaAlignLeft_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s02_BwaAlignRight_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s03_BwaSampe_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s04_SamToBam_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s05_SamSort_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s06_PicardQC_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s07_Markduplicates_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s08_RealignTargetCreator_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s09_Realign_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s10_Fixmates_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s11_CovariatesBefore_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s12_Recalibrate_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s13_SamSortRecal_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s14_CovariatesAfter_1.sh +# new file: modules/compute/demo/demoWorkflow/run00/s15_MergeBam_externalSampleID.sh +# new file: modules/compute/demo/demoWorkflow/run00/s16_PicardQCrecal_externalSampleID.sh +# new file: modules/compute/demo/demoWorkflow/run00/s17_UnifiedGenotyper_externalSampleID.sh +# new file: modules/compute/demo/demoWorkflow/run00/s18_GenomicAnnotator_externalSampleID.sh +# new file: modules/compute/demo/demoWorkflow/run00/s19_VariantAnnotator_externalSampleID.sh +# new file: modules/compute/demo/demoWorkflow/run00/s20_QCReport_projectName.sh +# new file: modules/compute/demo/demoWorkflow/run00/s20_QCReport_projectName.sh_WORKING_ON_MAC +# new file: modules/compute/demo/demoWorkflow/run00/submit.sh +# new file: modules/compute/demo/demoWorkflow/run00/workflow_ngs.csv +# new file: modules/compute/demo/demoWorkflow/run00/worksheet.csv +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/dataTransfer.sh +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/parameters.csv +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/runlocal.sh +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/s00_GenerateReference_1.sh +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/s01_IndexReference_1.sh +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/s02_DeployDbsnpIndelResources_projectName.sh +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/submit.sh +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/workflow_CreateAndDeployResources.csv +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/workflow_createReferenceGenome.csv +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/workflow_createReferenceGenomeAndReads.csv +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/workflow_createReferenceGenomeAndReads_csv.started +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/workflow_createReferenceGenome_csv.started +# new file: modules/compute/demo/demoWorkflow/runCreateRefGenomeAndReads/worksheet.csv +# new file: modules/compute/demo/demoWorkflow/source/1kg_pilot_release_merged_indels_sites_hg19_human_g1k_v37.vcf_header +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/Aligner.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/AnalyzeCovariates.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/CountRecords.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/GenomeAnalysisTK.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/IndexToTable.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/StingUtils.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/activation-1.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/annotations-1.3.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/aopalliance-1.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/bcel-5.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/bsh-2.0b4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/colt-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/commons-email-1.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/commons-io-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/commons-jexl-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/commons-lang-2.5.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/commons-logging-1.1.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/concurrent-1.3.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/dom4j-1.6.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/google-collections-1.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/gson-1.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/guice-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/jakarta-regexp-1.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/javassist-3.7.ga.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/javassist-3.8.0.GA.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/jcommander-1.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/jgrapht-jdk1.5-0.7.3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/jna-3.2.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/jsr305-1.3.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/junit-3.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/lucene-core-3.0.3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/mail-1.4.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/picard-1.37.686.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/picard-private-parts-1702.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/reflections-0.9.5-RC2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/sam-1.37.686.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/scala-compiler-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/scala-library-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/simple-xml-2.0.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/slf4j-api-1.5.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/snakeyaml-1.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/stax-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/stax-api-1.0.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/testng-5.14.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/testng-5.5-jdk15.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/tribble-0.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.0.5069/Sting/dist/xml-apis-1.0.b2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/LICENSE +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/build.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/Aligner.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/AnalyzeCovariates.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/GenomeAnalysisTK.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/StingUtils.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/activation-1.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/asm-all-3.3.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/bcel-5.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/cofoja-1.0-20110609.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/colt-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-codec-1.5.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-email-1.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-httpclient-3.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-io-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-jexl-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-lang-2.5.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-logging-1.1.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/commons-math-2.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/concurrent-1.3.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/dom4j-1.6.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/drmaa-6.2u5p2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/freemarker-2.3.18.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/google-collections-1.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/gson-1.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/jakarta-regexp-1.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/java-xmlbuilder-0.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/javassist-3.7.ga.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/javassist-3.8.0.GA.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/jets3t-0.8.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/jgrapht-jdk1.5-0.7.3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/jna-3.2.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/lucene-core-3.0.3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/mail-1.4.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/picard-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/picard-private-parts-2068.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/poi-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/poi-ooxml-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/poi-ooxml-schemas-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/reflections-0.9.5-RC2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/sam-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/scala-compiler-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/scala-library-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/simple-xml-2.0.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/slf4j-api-1.5.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/snakeyaml-1.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/snpeff-2.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/stax-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/stax-api-1.0.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/tribble-40.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/vcf.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/xml-apis-1.0.b2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/dist/xmlbeans-2.3.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/INDEX +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/Meta/Rd.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/Meta/data.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/Meta/hsearch.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/Meta/links.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/Meta/package.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/NAMESPACE +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/R/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/INDEX +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/Rd.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/data.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/hsearch.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/links.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/Meta/package.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/NAMESPACE +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/R/gsalib +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/R/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/R/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/AnIndex +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/aliases.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/help/paths.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/html/00Index.html +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/gsalib/html/R.css +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/help/AnIndex +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/help/aliases.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/help/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/help/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/help/paths.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/html/00Index.html +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib/html/R.css +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/gsalib_1.0.tar.gz +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/ivy.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/activation-1.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/asm-all-3.3.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/bcel-5.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/cofoja-1.0-20110609.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/colt-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-codec-1.5.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-email-1.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-httpclient-3.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-io-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-jexl-2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-lang-2.5.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-logging-1.1.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/commons-math-2.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/concurrent-1.3.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/dom4j-1.6.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/drmaa-6.2u5p2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/freemarker-2.3.18.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/google-collections-1.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/gson-1.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/jakarta-regexp-1.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/java-xmlbuilder-0.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/javassist-3.7.ga.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/javassist-3.8.0.GA.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/jets3t-0.8.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/jgrapht-jdk1.5-0.7.3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/jna-3.2.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/lucene-core-3.0.3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/mail-1.4.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/picard-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/picard-private-parts-2068.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/poi-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/poi-ooxml-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/poi-ooxml-schemas-3.8-beta3.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/reflections-0.9.5-RC2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/sam-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/scala-compiler-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/scala-library-2.8.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/simple-xml-2.0.4.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/slf4j-api-1.5.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/snakeyaml-1.7.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/snpeff-2.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/stax-1.2.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/stax-api-1.0.1.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/tribble-40.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/xml-apis-1.0.b2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/lib/xmlbeans-2.3.0.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/R.css +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/INDEX +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/Rd.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/data.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/hsearch.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/links.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/Meta/package.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/R/gsalib +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/R/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/R/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/AnIndex +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/aliases.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/gsalib.rdb +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/gsalib.rdx +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/help/paths.rds +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib/html/00Index.html +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/gsalib_1.0.tar.gz +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_OtherCovariate.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/analyzecovariates/plot_residualError_QualityScoreCovariate.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/data/tearsheetdrop.jpg +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/src/org/broadinstitute/sting/utils/R/gsalib_1.0.tar.gz +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/R/titvFPEst.R +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/SeparateQltout.cc +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/Makefile +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/build_linux.sh +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/build_mac.sh +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/bwa_gateway.cpp +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/bwa_gateway.h +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/libenvironhack/Makefile +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/libenvironhack/libenvironhack.c +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/c/libenvironhack/libenvironhack.dylib +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/b36tob37.chain +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/b37tob36.chain +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/b37tohg18.chain +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/b37tohg19.chain +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/hg18tob37.chain +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/hg19toHg18.chain +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/chainFiles/makeChains.py +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/doc/Ant_Help.tex +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/doc/GATK_Coding_Standards.pdf +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/doc/GATK_Coding_Standards.tex +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/doc/README +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKBAMFileSpan.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKBin.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKBinList.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/net/sf/samtools/GATKChunk.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/Aligner.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/Alignment.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAAligner.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/c/BWAPath.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedOutputStream.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalysisDataManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/analyzecovariates/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Advanced.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Argument.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinition.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSite.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ClassType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Gather.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Gatherer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Hidden.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Input.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/MissingArgumentValueException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Output.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/Tags.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/commandline/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/DownsampleType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/DownsamplingMethod.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMBlockStartIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMIndexContent.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMOverlap.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShard.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/MonolithicShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReaderBin.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategy.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardStrategyFactory.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/MicroSchedulerMBean.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/ReduceTree.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/executive/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/BadMateFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MaxReadLengthFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/Platform454Filter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/filters/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/Storage.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/Stub.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterStub.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/DownsampleIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/IterableIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/iterators/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTracker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumns.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Affection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Gender.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/PedigreeValidationType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/traversals/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Attribution.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/BAQMode.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/DataSource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Downsample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/DuplicateWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplex.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Multiplexer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionBy.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RMD.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Reference.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/RodWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BiallelicGenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidIndelGenotypePriors.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypePriors.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiallelicGenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SAMRecordCoordinateComparatorWithUnmappedReads.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/WriteVCF.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Dinuc.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatum.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDatumOptimized.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompEvalGenotypes.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PhaseStats.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SamplePreviousGenotypes.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/StateKey.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/TableType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/clibrary/JNAUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/clibrary/LibC.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobInfo.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobTemplate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSession.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionFactory.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaa.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/QueueVersion.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/queue/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/AminoAcid.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/AminoAcidTable.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/ContigComparator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/DisjointSet.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/HasGenomeLocation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/NGSPlatform.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/PathUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutorException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/Utils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/analysis/AminoAcid.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/analysis/AminoAcidTable.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/analysis/AminoAcidUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/IndexingVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/ManualSortingVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/SortingVCFWriterBase.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFNamedHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/ExpandingArrayList.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/NestedHashMap.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/Pair.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/PrimitivePair.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/collections/RODMergingIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/duplicates/DuplicateComp.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/DynamicClassResolutionException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/StingException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fasta/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/file/FileSystemInabilityToLockException.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentCollection.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFGenotype.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFHeaderBuilder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/gcf/GCFWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureObject.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/HelpFormatter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/IntervalMergingRule.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/IntervalSetRule.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/interval/OverlappingIntervalIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/FileExtension.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/HardThresholdingOutputStream.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/io/Resource.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ExtendedEventPileupElement.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementFilter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/pileup2/Notes +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/CapturedStreamOutput.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/InputStreamSettings.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/OutputStreamSettings.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/ProcessController.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/ProcessOutput.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/ProcessSettings.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/RuntimeUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/StreamLocation.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/runtime/StreamOutput.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ComparableSAMRecord.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/sam/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/text/XReadLines.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/threading/ThreadPoolMonitor.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/threading/package-info.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableGenotype.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/MutableVariantContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleHeader.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/yaml/FieldOrderComparator.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/yaml/StingYamlRepresenter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/src/org/broadinstitute/sting/utils/yaml/YamlUtils.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/net/sf/samtools/GATKChunkUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/BaseTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/MD5DB.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/StingTextReporter.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/WalkerTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/ArgumentMatchSiteUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/ArgumentMatchSourceUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/MockLocusShard.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMBAMDataSourceUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/executive/ReduceTreeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/ReadMetaDataTrackerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/clibrary/LibCUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/R/RScriptExecutorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/R/RScriptLibraryUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/ReservoirDownsamplerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/SimpleTimerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/collections/ExpandingArrayListUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/report/ReportMarshallerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/runtime/ProcessControllerUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/runtime/RuntimeUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/text/TextFormattingUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/threading/ThreadPoolMonitorUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/Aligner.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/AnalyzeCovariates.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/CreatePackager.xsl +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/GATK-Picard.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/GATKEngine.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/GenomeAnalysisTK.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/PicardPrivate.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/packages/Queue.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/perl/liftOverVCF.pl +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/perl/sortByRef.pl +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/Vcf2Table.q +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QException.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QScript.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/QSettings.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLineJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/CommandLinePluginManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/FunctionEdge.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/InProcessJobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/JobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/JobRunInfo.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/JobRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/MappingEdge.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QEdge.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/QNode.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/RunnerStatus.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/drmaa/DrmaaJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/gridengine/GridEngineJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobManager.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/AutoIndexGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/ExpandIntervals.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/intervals/IntersectIntervals.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/RetryException.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/scala/test/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/HiSeq.10000.bgzip.vcf.gz +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/HiSeq.10000.vcf +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/HiSeq.10000.vcf.gz +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/TabularDataTest.dat +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/TabularDataTest2.dat +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/ValidatingPileupTargets.list +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/ceutrio.ped +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/defaultGATKConfig.cfg +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/diffTestMaster.vcf +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/diffTestTest.vcf +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.bam +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.bam.bai +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.simple.bai +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleBAM.simple.bam +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleFASTA.dict +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleFASTA.fasta +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleFASTA.fasta.fai +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleNORG.bam +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/exampleNORG.bam.bai +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/gFFTest.gff +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/recalConfig_1KG.cfg +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/sampleBedFile.bed +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/small.dbsnp.rod +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/tranches.4.txt +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/tranches.6.txt +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/tranches.raw.dat +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/vcf/vcfWithGenotypes.vcf +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/public/testdata/vcf/vcfWithoutGenotypes.vcf +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/helpTemplates/common.html +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/helpTemplates/generic.index.template.html +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/helpTemplates/generic.template.html +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/helpTemplates/style.css +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/ivysettings.properties +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/ivysettings.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/edu.mit.broad/picard-private-parts-2068.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/edu.mit.broad/picard-private-parts-2068.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/gov.nist/Jama-1.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/gov.nist/Jama-1.0.2.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.snpeff/snpeff-2.0.2.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf.snpeff/snpeff-2.0.2.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/picard-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/picard-1.55.985.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/sam-1.55.985.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/net.sf/sam-1.55.985.xml +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/org.broad/tribble-40.jar +# new file: modules/compute/demo/demoWorkflow/source/GATK-1.3-24-gc8b1c92/settings/repository/org.broad/tribble-40.xml +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bntseq.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwape.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwase.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwaseqio.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwt.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwt_lite.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtaln.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtgap.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtindex.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtio.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtmisc.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtsw2_aux.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtsw2_chain.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtsw2_core.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/bwtsw2_main.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/cs2nt.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/is.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/kstring.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/main.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/simple_dp.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/stdaln.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/.deps/utils.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/20130129_simMachine_0001_FLOWCELL_L1_None_1.fq +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/AUTHORS +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/BWA_read_group_patch.diff +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/COPYING +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/ChangeLog +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/INSTALL +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/Makefile +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/Makefile.am +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/Makefile.in +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/NEWS +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/README +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/aclocal.m4 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/autogen.sh +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/autom4te.cache/output.0 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/autom4te.cache/output.1 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/autom4te.cache/requests +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/autom4te.cache/traces.0 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/autom4te.cache/traces.1 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bntseq.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bntseq.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwa +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwa.1 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwape.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwase.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwase.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwaseqio.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/.deps/QSufSort.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/.deps/bwt_gen.Po +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/Makefile +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/Makefile.am +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/Makefile.in +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/QSufSort.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/QSufSort.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/bwt_gen.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/bwt_gen.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_gen/libbwtgen.a +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_lite.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwt_lite.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtaln.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtaln.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtgap.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtgap.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtindex.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtio.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtmisc.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtsw2.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtsw2_aux.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtsw2_chain.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtsw2_core.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/bwtsw2_main.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/cleanup.sh +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/config.guess +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/config.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/config.h.in +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/config.log +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/config.status +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/config.sub +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/configure +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/configure.in +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/cs2nt.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/depcomp +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/install-sh +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/is.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/khash.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/kseq.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/ksort.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/kstring.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/kstring.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/kvec.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/libbwacore.a +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/m4/acx_pthread.m4 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/main.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/main.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/missing +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/out.sai +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/qualfa2fq.pl +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/simple_dp.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/solid2fastq.pl +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/sracsfq2fq.pl +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/stamp-h1 +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/stdaln.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/stdaln.h +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/utils.c +# new file: modules/compute/demo/demoWorkflow/source/bwa-0.5.8c_patched/utils.h +# new file: modules/compute/demo/demoWorkflow/source/createInsertSizePlot/createInsertSizePlot.R +# new file: modules/compute/demo/demoWorkflow/source/dbSNP135.tabdelim.table +# new file: modules/compute/demo/demoWorkflow/source/externalSampleID.concordance.ngsVSarray.txt +# new file: modules/compute/demo/demoWorkflow/source/getStatistics_20121127/NiceColumnNames.csv +# new file: modules/compute/demo/demoWorkflow/source/getStatistics_20121127/getStatistics.R +# new file: modules/compute/demo/demoWorkflow/source/picard-tools-1.61.tgz +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/AUTHORS +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/COPYING +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/ChangeLog +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/INSTALL +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/Makefile +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/Makefile.mingw +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/NEWS +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam2bcf.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam2bcf.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam2bcf_indel.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam2depth.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_aux.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_cat.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_color.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_endian.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_import.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_index.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_lpileup.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_mate.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_md.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_pileup.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_plcmd.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_reheader.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_rmdup.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_rmdupse.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_sort.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_stat.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bam_tview.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bamtk.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/Makefile +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/README +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/bcf.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/bcf.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/bcf.tex +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/bcf2qcall.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/bcftools +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/bcfutils.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/call1.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/em.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/fet.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/index.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/kfunc.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/kmin.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/kmin.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/libbcf.a +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/main.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/mut.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/prob1.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/prob1.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/vcf.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bcftools/vcfutils.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bedidx.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bgzf.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bgzf.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bgzip.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/blast2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/bowtie2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/cut_target.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/errmod.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/errmod.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/00README.txt +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/Makefile +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/bam2bed.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/calDepth.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/ex1.fa +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/ex1.sam.gz +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/toy.fa +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/examples/toy.sam +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/export2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/faidx.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/faidx.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/interpolate_sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kaln.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kaln.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/khash.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/klist.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/knetfile.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/knetfile.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kprobaln.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kprobaln.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kseq.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/ksort.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kstring.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/kstring.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/libbam.a +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/maq2sam-long +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/maq2sam-short +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/md5fa +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/md5sum-lite +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/HmmGlocal.java +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/Makefile +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/blast2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/bowtie2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/export2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/interpolate_sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam-long +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam-long.dSYM/Contents/Info.plist +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam-long.dSYM/Contents/Resources/DWARF/maq2sam-long +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam-short +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam-short.dSYM/Contents/Info.plist +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam-short.dSYM/Contents/Resources/DWARF/maq2sam-short +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/maq2sam.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/md5.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/md5.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/md5fa +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/md5fa.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/md5sum-lite +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/novo2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/psl2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/sam2vcf.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/samtools.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/seqtk +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/seqtk.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/soap2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/varfilter.py +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/wgsim +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/wgsim.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/wgsim_eval.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/misc/zoom2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/novo2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/phase.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/psl2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/razf.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/razf.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/razip.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sam.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sam.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sam2vcf.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sam_header.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sam_header.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sam_view.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sample.c +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/sample.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/samtools +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/samtools.1 +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/samtools.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/seqtk +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/soap2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/varfilter.py +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/vcfutils.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/wgsim +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/wgsim_eval.pl +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/win32/xcurses.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/win32/zconf.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/win32/zlib.h +# new file: modules/compute/demo/demoWorkflow/source/samtools-0.1.18/zoom2sam.pl +# new file: modules/compute/demo/demoWorkflow/source/scripts/createSNPTable_19mar2012/createSNPTable.R +# new file: modules/compute/demo/demoWorkflow/source/scripts/createSNPTable_19mar2012/createSNPTable.sh +# new file: modules/compute/demo/demoWorkflow/source/scripts/createSNPTable_19mar2012/createSNPTableFunctions.R +# new file: modules/compute/demo/demoWorkflow/source/scripts/createSNPTable_19mar2012/readCommandLineArgs.R +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/createDedupTableFunctions.R +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/getDedupInfo.R +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/getDedupInfo.sh +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/out.tex +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/readCommandLineArgs.R +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/run.sh +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/testdata/110303_SN163_0393_A80MP0ABXX_L4_AGAGAT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/testdata/110303_SN163_0393_A80MP0ABXX_L4_TAATTT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/testdata/111018_SN163_0434_AD0AP0ACXX_L5_AGAGAT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/testdata/111018_SN163_0434_AD0AP0ACXX_L5_TAATTT.human_g1k_v37.dedup.metrics +# new file: modules/compute/demo/demoWorkflow/source/scripts/getDedupInfo_23mar2012/testdata/getdata.sh +# new file: modules/compute/demo/demoWorkflow/source/scripts/import.sh +# new file: modules/compute/demo/demoWorkflow/templates/Footer.ftl +# new file: modules/compute/demo/demoWorkflow/templates/Header.ftl +# new file: modules/compute/demo/demoWorkflow/workflow_CreateAndDeployResources.csv +# new file: modules/compute/demo/demoWorkflow/workflow_DeployTools.csv +# new file: modules/compute/demo/demoWorkflow/workflow_ngs.csv +# new file: modules/compute/demo/demoWorkflow/worksheet.csv +# new file: modules/compute/demo/ebiogrid/ngs_worksheet.txt +# new file: modules/compute/demo/helloWorld/output/parameters.csv +# new file: modules/compute/demo/helloWorld/output/runlocal.sh +# new file: modules/compute/demo/helloWorld/output/s00_GuestInvitationStep_1.sh +# new file: modules/compute/demo/helloWorld/output/s00_GuestInvitationStep_2.sh +# new file: modules/compute/demo/helloWorld/output/s00_GuestInvitationStep_3.sh +# new file: modules/compute/demo/helloWorld/output/s00_GuestInvitationStep_4.sh +# new file: modules/compute/demo/helloWorld/output/s00_GuestInvitationStep_5.sh +# new file: modules/compute/demo/helloWorld/output/s01_OrganizerInvitationStep_adult.sh +# new file: modules/compute/demo/helloWorld/output/s01_OrganizerInvitationStep_child.sh +# new file: modules/compute/demo/helloWorld/output/submit.sh +# new file: modules/compute/demo/helloWorld/output/workflow.csv +# new file: modules/compute/demo/helloWorld/output/worksheet.csv +# new file: modules/compute/demo/helloWorld/protocols/Header.ftl +# new file: modules/compute/demo/helloWorld/system/Footer.ftl +# new file: modules/compute/demo/helloWorld/system/Header.ftl +# new file: modules/compute/demo/helloWorld/system/Submit.sh.ftl +# new file: modules/compute/demo/minimacV2/workflow1/output/parameters.csv +# new file: modules/compute/demo/minimacV2/workflow1/output/runlocal.sh +# new file: modules/compute/demo/minimacV2/workflow1/output/s00_prepare_s00_1.sh +# new file: modules/compute/demo/minimacV2/workflow1/output/s01_prepare_s01_FALSE.sh +# new file: modules/compute/demo/minimacV2/workflow1/output/submit.sh +# new file: modules/compute/demo/minimacV2/workflow1/output/workflow.csv +# new file: modules/compute/demo/minimacV2/workflow1/output/worksheet.csv +# new file: modules/compute/demo/minimacV2/workflow1/parameters.csv +# new file: modules/compute/demo/minimacV2/workflow1/protocols/CustomSubmit.sh.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/Footer.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/Header.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/Helpers.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/Macros.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/NGSHeader.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/Submit.sh.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/mergeMinimacImputationResults.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/minimacImputation.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/phaseChunk.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/prepareStudy.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/startMinimacStage2.ftl +# new file: modules/compute/demo/minimacV2/workflow1/protocols/startMinimacStage3.ftl +# new file: modules/compute/demo/minimacV2/workflow1/workflow.csv +# new file: modules/compute/demo/minimacV2/workflow1/worksheet.csv +# new file: modules/compute/demo/variantTableInQCReport/output/parameters.csv +# new file: modules/compute/demo/variantTableInQCReport/output/runlocal.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s00_BwaAlignLeft_1.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s01_BwaAlignRight_1.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s02_BwaSampe_1.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s03_SamToBam_1.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s04_SamSort_1.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s05_PicardQC_1.sh +# new file: modules/compute/demo/variantTableInQCReport/output/s06_QCReport_projectName.sh +# new file: modules/compute/demo/variantTableInQCReport/output/submit.sh +# new file: modules/compute/demo/variantTableInQCReport/output/workflow.csv +# new file: modules/compute/demo/variantTableInQCReport/output/workflow_csv.started +# new file: modules/compute/demo/variantTableInQCReport/output/worksheet.csv +# new file: modules/compute/demo/variantTableInQCReport/parameters.csv +# new file: modules/compute/demo/variantTableInQCReport/protocols/BwaAlignLeft.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/BwaAlignRight.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/BwaSampe.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/Helpers.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/PicardQC.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/QCReport.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/QCReportTemplate.tex +# new file: modules/compute/demo/variantTableInQCReport/protocols/SamSort.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/SamToBam.ftl +# new file: modules/compute/demo/variantTableInQCReport/protocols/Submit.sh.ftl +# new file: modules/compute/demo/variantTableInQCReport/root/data/simulatedLeft.fq.gz +# new file: modules/compute/demo/variantTableInQCReport/root/data/simulatedRight.fq.gz +# new file: modules/compute/demo/variantTableInQCReport/root/data/visualization.txt +# new file: modules/compute/demo/variantTableInQCReport/root/resources/createDictionary.sh +# new file: modules/compute/demo/variantTableInQCReport/root/resources/createIndex.sh +# new file: modules/compute/demo/variantTableInQCReport/root/resources/create_interval_list.sh +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.dict +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.amb +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.ann +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.bwt +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.pac +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.rbwt +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.rpac +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.rsa +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/indices/simulatedReferenceGenome.fa.sa +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/intervals/simulated_baits.bed +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/intervals/simulated_baits.interval_list +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/intervals/simulated_targets.bed +# new file: modules/compute/demo/variantTableInQCReport/root/resources/hg19/intervals/simulated_targets.interval_list +# new file: modules/compute/demo/variantTableInQCReport/root/resources/simRefGenome.R +# new file: modules/compute/demo/variantTableInQCReport/root/resources/simulate_bedFiles.bash.sh +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/AUTHORS +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/BWA_read_group_patch.diff +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/COPYING +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/ChangeLog +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/INSTALL +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/Makefile +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/Makefile.am +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/NEWS +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/README +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/autogen.sh +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bntseq.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bntseq.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwa +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwa.1 +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwape.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwase.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwase.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwaseqio.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/Makefile +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/Makefile.am +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/QSufSort.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/QSufSort.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/bwt_gen.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/bwt_gen.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_gen/libbwtgen.a +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_lite.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwt_lite.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtaln.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtaln.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtgap.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtgap.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtindex.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtio.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtmisc.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtsw2.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtsw2_aux.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtsw2_chain.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtsw2_core.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/bwtsw2_main.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/cleanup.sh +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/config.h.in +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/configure.in +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/cs2nt.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/is.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/khash.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/kseq.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/ksort.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/kstring.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/kstring.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/kvec.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/m4/acx_pthread.m4 +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/main.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/main.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/qualfa2fq.pl +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/simple_dp.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/solid2fastq.pl +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/sracsfq2fq.pl +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/stdaln.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/stdaln.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/utils.c +# new file: modules/compute/demo/variantTableInQCReport/root/tools/bwa-0.5.8c_patched/utils.h +# new file: modules/compute/demo/variantTableInQCReport/root/tools/getTools.sh +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61.tgz +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/AddOrReplaceReadGroups.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/BamIndexStats.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/BamToBfq.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/BuildBamIndex.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CalculateHsMetrics.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CleanSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CollectAlignmentSummaryMetrics.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CollectGcBiasMetrics.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CollectInsertSizeMetrics.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CollectMultipleMetrics.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CollectRnaSeqMetrics.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CompareSAMs.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/CreateSequenceDictionary.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/DownsampleSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/EstimateLibraryComplexity.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/ExtractIlluminaBarcodes.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/ExtractSequences.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/FastqToSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/FilterSamReads.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/FixMateInformation.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/IlluminaBasecallsToSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/IntervalListTools.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/MarkDuplicates.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/MeanQualityByCycle.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/MergeBamAlignment.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/MergeSamFiles.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/NormalizeFasta.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/QualityScoreDistribution.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/ReorderSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/ReplaceSamHeader.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/RevertSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/SamFormatConverter.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/SamToFastq.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/SortSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/ValidateSamFile.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/ViewSam.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/picard-1.61.jar +# new file: modules/compute/demo/variantTableInQCReport/root/tools/picard-tools-1.61/sam-1.61.jar +# new file: modules/compute/demo/variantTableInQCReport/workflow.csv +# new file: modules/compute/demo/variantTableInQCReport/worksheet.csv +# +# Changes not staged for commit: +# (use "git add ..." to update what will be committed) +# (use "git checkout -- ..." to discard changes in working directory) +# +# modified: .gitignore +# +# Untracked files: +# (use "git add ..." to include in what will be committed) +# +# status.txt