Merge pull request #41 from Gerbenvandervries/master

minor bugfixes for autotest
molgenis · Jun 19, 2023 · 90c16ab · 90c16ab
2 parents 695d1af + a336c83
commit 90c16ab
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-<h1> NGS_RNA pipeline</h1>
+<h1>NGS_RNA pipeline</h1>
 
 <h2>Description of the different steps used in the RNA analysis pipeline </h2>
 

diff --git a/check/shellcheck.sh b/check/shellcheck.sh
@@ -7,10 +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.
-#  * SC2148  Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive. Not needed for Molgenis Compute protocols.
-#  * SC2154  Not deeded, Molgenis Compute takes care of this.
+#  * SC2154: Due to Molgenis Compute string initialization the warning is not valid 
 #
-export SHELLCHECK_OPTS="-e SC2004 -e SC2015 -e SC2148 -e SC2154"
+#  * 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() {
 	#
@@ -33,7 +35,7 @@ EOH
 #
 # Parse commandline options
 #
-while getopts "hv" opt
+while getopts ":hv" opt
 do
 	case "${opt}" in
 		h)
@@ -89,7 +91,8 @@ then
 	#	https://github.com/koalaman/shellcheck/wiki/SC${ISSUENUMBER}
 	# 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='&lt;a href=&quot;https://github.com/koalaman/shellcheck/wiki/\$2&quot;&gt;\$2: \$1&lt;/a&gt;' source='ShellCheck.\$2'|" checkstyle-result.xml
+	perl -pi -e "s|message='([^']+)'\s+source='ShellCheck.(SC[0-9]+)'|message='&lt;a href=&quot;https://github.com/koalaman/shellcheck/wiki/\$2&quot;&gt;\$2: 
+\$1&lt;/a&gt;' source='ShellCheck.\$2'|" checkstyle-result.xml
 else
 	#
 	# ShellCheck for regular user on the commandline.

diff --git a/parameters.fender.csv b/parameters.fender.csv
@@ -7,3 +7,38 @@ root,/apps/
 tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm10
 toolchain,foss-2018b
+GCCcoreVersion,GCCcore-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/22.10.1
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/3.6.1-${toolchain}-bare
+rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
+picardVersion,picard/2.20.5-Java-11-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
diff --git a/parameters.gearshift.csv b/parameters.gearshift.csv
@@ -7,3 +7,38 @@ root,/apps/
 tempDir,${workDir}/${tmpName}/tmp/
 permanentDir,${workDir}/prm03
 toolchain,foss-2018b
+GCCcoreVersion,GCCcore-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/22.10.1
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/3.6.1-${toolchain}-bare
+rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
+picardVersion,picard/2.20.5-Java-11-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
diff --git a/parameters.homo_sapiens.GRCh37.csv b/parameters.homo_sapiens.GRCh37.csv
@@ -3,42 +3,6 @@ stage,module load
 checkStage,module list
 jobname,jobname
 
-##### Tools and versions #####
-jdkVersion,Java/8-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-GCCcore-7.3.0
-ngsRNAVersion,NGS_RNA/beta
-fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-GCCcore-7.3.0
-bedToolsVersion,BEDTools/2.28.0-GCCcore-7.3.0
-sambambaVersion,sambamba/0.7.0
-rVersion,R/3.6.1-${toolchain}-bare
-rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
-picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-GCCcore-7.3.0-Python-3.7.4
-hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-GCCcore-7.3.0
-pythonVersion,Python/3.7.4-GCCcore-7.3.0-bare
-python2Version,Python/2.7.16-GCCcore-7.3.0-bare
-python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
-pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
-gatkVersion,GATK/4.1.4.1-Java-8-LTS
-multiqcVersion,multiqc_v1.12.sif
-wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
-anacondaVersion,Anaconda/1.8.0-Linux-x86_64
-starVersion,STAR/2.7.3a-${toolchain}
-picardJar,picard.jar
-gatkJar,gatk-package-4.1.4.1-local.jar
-mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-GCCcore-7.3.0-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-GCCcore-7.3.0-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-GCCcore-7.3.0-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-foss-2018b
-vipVersion,vip/v3.3.1-foss-2018b
-outriderVersion,outrider_latest.sif
-rMATsVersion,rmats_v4.1.2.sif
-sifDir,/apps/data/GAD/singularity/
-rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
-
 ##### GENERAL DIRECTORIES #####
 tmpDataDir,${workDir}/${tmpName}/
 tmpTmpDataDir,${tmpDataDir}/tmp/
@@ -150,7 +114,7 @@ qcMatrics,${intermediateDir}/${externalSampleID}.total.qc.metrics.table
 ##### Protocols 3,6  (HTSeq count, MakeExpressionTable) #####
 sampleHTseqExpressionText,${intermediateDir}/${externalSampleID}.counts.txt
 projectHTseqExpressionTable,${intermediateDir}/${project}.expression.counts.table
-rnaSeQCGTF,/groups/umcg-solve-rd/tmp01/resources/GAD/gtf/gencode.v19.annotation.patched_contigs.genes.gtf
+rnaSeQCGTF,/apps/data/GAD/gtf/gencode.v19.annotation.patched_contigs.genes.gtf
 rnaSeQCDir,${projectResultsDir}/RNASeQC
 
 ##### GENOME,INDEX,ANNOTATION FILES #####

diff --git a/parameters.homo_sapiens.GRCh37.solve-rd.csv b/parameters.homo_sapiens.GRCh37.solve-rd.csv
@@ -3,42 +3,6 @@ stage,module load
 checkStage,module list
 jobname,jobname
 
-##### Tools and versions #####
-jdkVersion,Java/8-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-GCCcore-7.3.0
-ngsRNAVersion,NGS_RNA/beta
-fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-GCCcore-7.3.0
-bedToolsVersion,BEDTools/2.28.0-GCCcore-7.3.0
-sambambaVersion,sambamba/0.7.0
-rVersion,R/3.6.1-${toolchain}-bare
-rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
-picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-GCCcore-7.3.0-Python-3.7.4
-hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-GCCcore-7.3.0
-pythonVersion,Python/3.7.4-GCCcore-7.3.0-bare
-python2Version,Python/2.7.16-GCCcore-7.3.0-bare
-python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
-pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
-gatkVersion,GATK/4.1.4.1-Java-8-LTS
-multiqcVersion,multiqc_v1.12.sif
-wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
-anacondaVersion,Anaconda/1.8.0-Linux-x86_64
-starVersion,STAR/2.7.3a-${toolchain}
-picardJar,picard.jar
-gatkJar,gatk-package-4.1.4.1-local.jar
-mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-GCCcore-7.3.0-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-GCCcore-7.3.0-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-GCCcore-7.3.0-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-foss-2018b
-vipVersion,vip/v3.3.1-foss-2018b
-outriderVersion,outrider_latest.sif
-rMATsVersion,rmats_v4.1.2.sif
-sifDir,/groups/umcg-solve-rd/tmp01/resources/GAD/singularity/
-rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
-
 ##### GENERAL DIRECTORIES #####
 tmpDataDir,/groups/umcg-solve-rd/tmp01/rna/
 tmpTmpDataDir,/groups/umcg-solve-rd/tmp01/rna/tmp/
@@ -188,3 +152,4 @@ annotationFile,${dataDir}Ensembl/GrCh37.75/pub/release-75/gtf/${speciesFileName}
 ensembleDir,${dataDir}/ftp.broadinstitute.org/bundle/2.8/${genome}/gtf/${speciesFileName}/
 spliceaiSnv,/apps/data/SpliceAI/GRCh37/spliceai_scores.raw.snv.vcf.gz
 spliceaiIndel,/apps/data/SpliceAI/GRCh37/spliceai_scores.raw.indel.vcf.gz
+leafcutterAllExon,/apps/data/GAD/others/gencode_GRCh37_all_exons.txt.gz
diff --git a/parameters.homo_sapiens.hg19.solve-rd.csv b/parameters.homo_sapiens.hg19.solve-rd.csv
@@ -4,39 +4,37 @@ checkStage,module list
 jobname,jobname
 
 ##### Tools and versions #####
-jdkVersion,Java/8-LTS
-ngsUtilsVersion,ngs-utils/19.03.3-GCCcore-7.3.0
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/19.03.3-${GCCcoreVersion}
 ngsRNAVersion,NGS_RNA/beta
 fastqcVersion,FastQC/0.11.8-Java-11-LTS
-samtoolsVersion,SAMtools/1.9-GCCcore-7.3.0
-bedToolsVersion,BEDTools/2.28.0-GCCcore-7.3.0
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
 sambambaVersion,sambamba/0.7.0
 rVersion,R/3.6.1-${toolchain}-bare
 rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
 picardVersion,picard/2.20.5-Java-11-LTS
-htseqVersion,HTSeq/0.11.0-GCCcore-7.3.0-Python-3.7.4
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
 hisatVersion,hisat2/2.1.0-${toolchain}
-htsLibVersion,HTSlib/1.11-GCCcore-7.3.0
-pythonVersion,Python/3.7.4-GCCcore-7.3.0-bare
-python2Version,Python/2.7.16-GCCcore-7.3.0-bare
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
 python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
 pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
 gatkVersion,GATK/4.1.4.1-Java-8-LTS
 multiqcVersion,multiqc_v1.12.sif
-wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
-anacondaVersion,Anaconda/1.8.0-Linux-x86_64
 starVersion,STAR/2.7.3a-${toolchain}
 picardJar,picard.jar
 gatkJar,gatk-package-4.1.4.1-local.jar
 mergeSamFilesJar,MergeSamFiles
-trimGaloreVersion,TrimGalore/0.4.5-GCCcore-7.3.0-Python-3.7.4-bare
-cutadaptVersion,cutadapt/2.6-GCCcore-7.3.0-Python-3.7.4-bare
-rSeQCVersion,RSeQC/3.0.1-GCCcore-7.3.0-Python-3.7.4
-leafcutterVersion,leafcutter/aa12b1e-foss-2018b
-vipVersion,vip/v3.3.1-foss-2018b
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
 outriderVersion,outrider_latest.sif
 rMATsVersion,rmats_v4.1.2.sif
-sifDir,/groups/umcg-solve-rd/tmp01/resources/GAD/singularity/
+sifDir,/apps/data/GAD/singularity/
 rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
 
 ##### GENERAL DIRECTORIES #####

diff --git a/parameters.hyperchicken.csv b/parameters.hyperchicken.csv
@@ -0,0 +1,45 @@
+#### ENVIRONMENT VARIABLES ####
+queue,atd
+workDir,/groups/${groupname}/
+dataDir,${root}/data/
+tmpName,tmp09
+root,/apps/
+tempDir,${workDir}/${tmpName}/tmp/
+permanentDir,${workDir}/prm03
+toolchain,foss-2022a
+GCCcoreVersion,GCCcore-11.3.0
+GCCVersion,GCC-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/22.10.1
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.16.1-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.30.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/4.2.1-${toolchain}-bare
+rPlusVersion,RPlus/4.2.1-${toolchain}-v23.01.1
+picardVersion,picard/2.26.10-Java-8-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.10.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.16-${GCCcoreVersion}
+pythonVersion,Python/3.10.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-foss-2018b-v21.08.1
+pythonPlusVersion,PythonPlus/3.10.4-${toolchain}-v22.11.3
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-GCC-11.3.0
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.6.7-${GCCcoreVersion}
+cutadaptVersion,cutadapt/4.2-${GCCcoreVersion}-Python-3.10.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.10.4
+leafcutterVersion,leafcutter/aa12b1e-${GCCcoreVersion}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
diff --git a/parameters.talos.csv b/parameters.talos.csv
@@ -0,0 +1,44 @@
+#### ENVIRONMENT VARIABLES ####
+queue,atd
+workDir,/groups/${groupname}/
+dataDir,${root}/data/
+tmpName,tmp01
+root,/apps/
+tempDir,${workDir}/${tmpName}/tmp/
+permanentDir,${workDir}/prm08
+toolchain,foss-2022a
+GCCcoreVersion,GCCcore-11.3.0
+
+##### Tools and versions #####
+jdkVersion,Java/11-LTS
+ngsUtilsVersion,ngs-utils/22.10.1
+ngsRNAVersion,NGS_RNA/beta
+fastqcVersion,FastQC/0.11.8-Java-11-LTS
+samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
+bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
+sambambaVersion,sambamba/0.7.0
+rVersion,R/3.6.1-${toolchain}-bare
+rPlusVersion,RPlus/3.6.1-${toolchain}-v21.10.1
+picardVersion,picard/2.20.5-Java-11-LTS
+htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
+hisatVersion,hisat2/2.1.0-${toolchain}
+htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
+pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
+python2Version,Python/2.7.16-${GCCcoreVersion}-bare
+python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
+pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
+gatkVersion,GATK/4.1.4.1-Java-8-LTS
+multiqcVersion,multiqc_v1.12.sif
+starVersion,STAR/2.7.3a-${toolchain}
+picardJar,picard.jar
+gatkJar,gatk-package-4.1.4.1-local.jar
+mergeSamFilesJar,MergeSamFiles
+trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
+cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
+rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
+leafcutterVersion,leafcutter/aa12b1e-${toolchain}
+vipVersion,vip/v3.3.1-${toolchain}
+outriderVersion,outrider_latest.sif
+rMATsVersion,rmats_v4.1.2.sif
+sifDir,/apps/data/GAD/singularity/
+rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif
diff --git a/protocols/AddOrReplaceReadGroups.sh b/protocols/AddOrReplaceReadGroups.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+set -o pipefail
 #MOLGENIS nodes=1 ppn=8 mem=8gb walltime=05:00:00
 
 #string project
@@ -32,7 +32,6 @@ module load "${picardVersion}"
 #check modules
 module list
 
-echo "## $(date) Start $0"
 
 java -Xmx6g -XX:ParallelGCThreads=8 -jar "${EBROOTPICARD}/${picardJar}" AddOrReplaceReadGroups \
 I="${sortedBam}" \
@@ -43,7 +42,6 @@ RGLB="${externalSampleID}" \
 RGPL=ILLUMINA \
 RGPU="${sequencer}_${flowcell}_${run}" \
 RGSM="${externalSampleID}" \
-RGDT=$(date --rfc-3339=date) \
 CREATE_INDEX=true \
 MAX_RECORDS_IN_RAM=4000000 \
 TMP_DIR="${tempDir}"
@@ -52,4 +50,3 @@ echo "returncode: $?";
 mv "${tmpAddOrReplaceGroupsBam}" "${addOrReplaceGroupsBam}"
 mv "${tmpAddOrReplaceGroupsBai}" "${addOrReplaceGroupsBai}"
 echo "succes moving files";
-echo "## $(date) ##  $0 Done "