From 4140c55a67b8cf2f0e1aa25433389c0bd2ac582c Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 4 Feb 2022 15:45:16 +0100 Subject: [PATCH 1/3] Create parameters_wingedhelix.csv --- parameters_wingedhelix.csv | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 parameters_wingedhelix.csv diff --git a/parameters_wingedhelix.csv b/parameters_wingedhelix.csv new file mode 100644 index 00000000..27a2c26c --- /dev/null +++ b/parameters_wingedhelix.csv @@ -0,0 +1,7 @@ +queue,wh-vcompute +prmName,prm07 +prmHost,wh-helper.hpc.rug.nl +root,/ +appsDir,${root}/apps/ +toolChain_max,foss-2018b +toolChain_min,GCCcore-7.3.0 From ac8907862524daf758619047ce91ab1b28f463d0 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 4 Feb 2022 15:47:48 +0100 Subject: [PATCH 2/3] Update parameters.csv --- parameters.csv | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/parameters.csv b/parameters.csv index 3c86307a..6acb096f 100644 --- a/parameters.csv +++ b/parameters.csv @@ -10,28 +10,27 @@ gavinPlusJar,gavin-plus-1.5.0-RELEASE.jar picardJar,picard.jar vepDBVersion,92 vepAssemblyVersion,GRCh37 -bcfToolsVersion,BCFtools/1.14-${toolChain_min} -bedToolsVersion,BEDTools/2.30.0-${toolChain_min} +bcfToolsVersion,BCFtools/1.14-${toolChain_max} +bedToolsVersion,BEDTools/2.30.0-${toolChain_max} bwaVersion,BWA/0.7.17-${toolChain_min} -computeVersion,Molgenis-Compute/v19.01.1-Java-11-LTS -caddVersion,CADD/v1.4-foss-2018b +computeVersion,Molgenis-Compute/v19.01.1-Java-8-LTS +caddVersion,CADD/v1.4-${toolChain_max} convadingVersion,1.2.1-${toolChain_min} -cutadaptVersion,cutadapt/1.13-${toolChain_max}-Python-2.7.10 fastqcVersion,FastQC/0.11.9-Java-8-LTS gatkVersion,GATK/4.2.4.1-Java-8-LTS -gavinPlusVersion,gavin-plus/1.5.0-Java-11-LTS +gavinPlusVersion,gavin-plus/1.5.0-Java-8-LTS hashdeepVersion,hashdeep/4.4-foss-2015b htsLibVersion,HTSlib/1.14-${toolChain_min} iolibVersion,io_lib/1.14.11-${toolChain_min} javaVersion,Java/8-LTS mantaVersion,manta/1.6.0-${toolChain_min} -multiQCVersion,multiqc/1.11-${toolChain_min}-Python-3.7.4-bare +multiQCVersion,multiqc/1.11-${toolChain_max} ngsUtilsVersion,ngs-utils/19.03.3-${toolChain_min} perlPlusVersion,PerlPlus/5.30.0-${toolChain_min}-v19.08.1 plink1Version,PLINK/1.07-x86_64 plink2Version,plink/1.9-beta6-20190617 plinkSeqVersion,plinkseq/x86_64-0.10 -picardVersion,picard/2.26.10-Java-11-LTS +picardVersion,picard/2.26.10-Java-8-LTS pigzVersion,pigz/2.7-${toolChain_min} rVersion,R/3.6.1-${toolChain_max}-bare sambambaVersion,sambamba/0.7.0 From d84c3c44c13f5e33f9ebb142687f0f0ec82680d5 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Fri, 4 Feb 2022 15:59:02 +0100 Subject: [PATCH 3/3] Update parameters.csv --- parameters.csv | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/parameters.csv b/parameters.csv index 6acb096f..46d9c99b 100644 --- a/parameters.csv +++ b/parameters.csv @@ -4,6 +4,8 @@ targetedInsertSize,200 checkStage,module list ### Tool versions #### +javaSuffix,Java-8-LTS +javaVersion,Java/8-LTS hpoVersion,90 gatkJar,gatk-package-4.2.4.2-local.jar gavinPlusJar,gavin-plus-1.5.0-RELEASE.jar @@ -13,34 +15,30 @@ vepAssemblyVersion,GRCh37 bcfToolsVersion,BCFtools/1.14-${toolChain_max} bedToolsVersion,BEDTools/2.30.0-${toolChain_max} bwaVersion,BWA/0.7.17-${toolChain_min} -computeVersion,Molgenis-Compute/v19.01.1-Java-8-LTS +computeVersion,Molgenis-Compute/v19.01.1-${javaSuffix} caddVersion,CADD/v1.4-${toolChain_max} convadingVersion,1.2.1-${toolChain_min} -fastqcVersion,FastQC/0.11.9-Java-8-LTS -gatkVersion,GATK/4.2.4.1-Java-8-LTS -gavinPlusVersion,gavin-plus/1.5.0-Java-8-LTS -hashdeepVersion,hashdeep/4.4-foss-2015b -htsLibVersion,HTSlib/1.14-${toolChain_min} +fastqcVersion,FastQC/0.11.9-${javaSuffix} +gatkVersion,GATK/4.2.4.1-${javaSuffix} +gavinPlusVersion,gavin-plus/1.5.0-${javaSuffix} +hashdeepVersion,hashdeep/4.4-${toolChain_max} +htsLibVersion,HTSlib/1.14-${toolChain_max} iolibVersion,io_lib/1.14.11-${toolChain_min} -javaVersion,Java/8-LTS mantaVersion,manta/1.6.0-${toolChain_min} multiQCVersion,multiqc/1.11-${toolChain_max} -ngsUtilsVersion,ngs-utils/19.03.3-${toolChain_min} +ngsUtilsVersion,ngs-utils/22.01.1 perlPlusVersion,PerlPlus/5.30.0-${toolChain_min}-v19.08.1 plink1Version,PLINK/1.07-x86_64 plink2Version,plink/1.9-beta6-20190617 plinkSeqVersion,plinkseq/x86_64-0.10 -picardVersion,picard/2.26.10-Java-8-LTS -pigzVersion,pigz/2.7-${toolChain_min} -rVersion,R/3.6.1-${toolChain_max}-bare +picardVersion,picard/2.26.10-${javaSuffix} +pigzVersion,pigz/2.7-${toolChain_max} sambambaVersion,sambamba/0.7.0 -samtoolsVersion,SAMtools/1.14-${toolChain_min} +samtoolsVersion,SAMtools/1.14-${toolChain_max} seqTkVersion,seqtk/1.3-${toolChain_min} -snpEffVersion,snpEff/4.3t-Java-11-LTS +snpEffVersion,snpEff/4.3t-Java-${javaSuffix} vcfAnnoVersion,vcfanno/v0.3.3 vepVersion,VEP/90.5 -verifyBamIDVersion,verifyBamID/1.1.3-${toolChain_min} -xhmmVersion,xhmm/2016-01-04-cc14e528d909-${toolChain_max} ##### GENERAL DIRECTORIES ##### dataDir,${appsDir}/data/