WIP

check/indentationcheck.sh

@@ -3,7 +3,7 @@
 #
 # Use either WORKSPACE location for Jenkins or
 # resolve path to scripts we need to check
-# when executed manualy outside Jenkins.
+# when executed manually outside Jenkins.
 #
 if [[ -z "${WORKSPACE:-}" ]]; then
 	MYDIR="$(cd -P "$(dirname "${0}")" && pwd)"
@@ -13,7 +13,7 @@ fi
 echo '#####################################################################################'
 echo '  Bash code must be indented with TABs. Checking for lines indented with spaces ... '
 echo '#####################################################################################'
-grep -n '^[[:space:]]* [[:space:]]*' "${WORKSPACE:-../}/protocols/"*.*sh
+grep -n '^[[:space:]]* [[:space:]]*' "${WORKSPACE:-../}"/{protocols,scripts}/*.*sh
 grep_exit_status="${?}"
 if [[ "${grep_exit_status}" -eq 0 ]]; then
 	echo '#####################################################################################'

check/shellcheck.sh

@@ -7,8 +7,12 @@
 #  * SC2015: Note that A && B || C is not if-then-else. C may run when A is true.
 #            We know and use this construct regularly to create "transactions"
 #            where C is only executed when both A and B have succeeded.
+#  * SC2154: Due to Molgenis Compute string initialization the warning is not valid 
 #
-export SHELLCHECK_OPTS="-e SC2004 -e SC2015"
+#  * SC2148: the shebang is declared in the header.ftl not in the protocols
+#
+
+export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2154 -e SC2148"
 
 function showHelp() {
 	#
@@ -85,7 +89,7 @@ then
 	#
 	# Reformat the generated report to add hyperlinks to the ShellCheck issues on the wiki:
 	#	https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER}
-	# explaining whatis wrong with the code / style and how to improve it.
+	# explaining what is wrong with the code / style and how to improve it.
 	#
 	perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='<a href="https://github.com/koalaman/shellcheck/wiki/\$2">\$2: \$1</a>' source='ShellCheck.\$2'|" checkstyle-result.xml
 else
@@ -96,7 +100,7 @@ else
 	if [[ "${verbose:-0}" -eq 1 ]]
 	then
 		cd "${MYDIR}/.."
-		shellcheck -a -x -o all -f tty bin/*.sh # cannot use the printf construct used below for non-vebose output as it destroys the terminal colors.
+		shellcheck -a -x -o all -f tty protocols/*.sh # cannot use the printf construct used below for non-vebose output as it destroys the terminal colors.
 		cd '-' # Goes back to previous directory before we changed to ${MYDIR}.
 	else
 		printf '%s\n' "$(cd "${MYDIR}/.." && shellcheck -a -x -o all -f gcc protocols/*.sh)"

generate_template.sh

@@ -50,13 +50,13 @@ if [[ -n "${_sampleSheetColumnOffsets["barcode"]+isset}" ]]; then
 fi
 
 ## Will return or nothing or in case there is a dualbarcode it will create a file
-perl "${EBROOTNGS_DEMULTIPLEXING}/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DEMULTIPLEXING}/parameters.csv" > \
+perl "${EBROOTNGS_DEMULTIPLEXING}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DEMULTIPLEXING}/parameters.csv" > \
 "${WORKDIR}/generatedscripts/NGS_Demultiplexing/${RAWDATANAME}/out.csv"
 
-perl "${EBROOTNGS_DEMULTIPLEXING}/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DEMULTIPLEXING}/${ENVIRONMENT_PARAMETERS}" > \
+perl "${EBROOTNGS_DEMULTIPLEXING}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DEMULTIPLEXING}/${ENVIRONMENT_PARAMETERS}" > \
 "${WORKDIR}/generatedscripts/NGS_Demultiplexing/${RAWDATANAME}/environment_parameters.csv"
 
-perl "${EBROOTNGS_DEMULTIPLEXING}/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DEMULTIPLEXING}/parameters_${GROUP}.csv" > \
+perl "${EBROOTNGS_DEMULTIPLEXING}/scripts/convertParametersGitToMolgenis.pl" "${EBROOTNGS_DEMULTIPLEXING}/parameters_${GROUP}.csv" > \
 "${WORKDIR}/generatedscripts/NGS_Demultiplexing/${RAWDATANAME}/parameters_group.csv"
 
 bash "${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh" \

parameters.csv

@@ -3,7 +3,7 @@ stage,module load
 checkStage,module list
 
 ### Tool versions ####
-bcl2fastqVersion,bcl2fastq2/2.20.0-foss-2022a
+bcl2fastqVersion,bcl2fastq2/2.20.0-GCC-11.3.0
 perlPlusVersion,PerlPlus/5.34.1-GCCcore-11.3.0-v22.11.1
 interopVersion,interop/1.2.0-foss-2022a
 

protocols/Bcl2FastQ.sh

@@ -1,4 +1,4 @@
-#MOLGENIS walltime=12:00:00 nodes=1 ppn=6 mem=12gb
+#MOLGENIS walltime=12:00:00 nodes=1 ppn=6 mem=20gb
 #string bcl2fastqVersion
 #string nextSeqRunDataDir
 #string stage
@@ -46,15 +46,15 @@ module load "${demultiplexingversion}"
 if [[ "${dualBarcode}" == 'TRUE' ]]
 then
 	echo 'dualBarcode modus on'
-	perl "${EBROOTNGS_DEMULTIPLEXING}/CreateIlluminaSampleSheet_V3.pl" \
+	perl "${EBROOTNGS_DEMULTIPLEXING}/scripts/CreateIlluminaSampleSheet_V3.pl" \
 	-i "${sampleSheet}" \
 	-o "${tmpIntermediateDir}/Illumina_R${run}.csv" \
 	-r "${run}" \
 	-d TRUE \
 	-s "${prepKitsDir}"
 else
 	echo 'only one barcode detected'
-	perl "${EBROOTNGS_DEMULTIPLEXING}/CreateIlluminaSampleSheet_V2.pl" \
+	perl "${EBROOTNGS_DEMULTIPLEXING}/scripts/CreateIlluminaSampleSheet_V2.pl" \
 	-i "${sampleSheet}" \
 	-o "${tmpIntermediateDir}/Illumina_R${run}.csv" \
 	-r "${run}" \