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maxulyssemaxulysse
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Merge pull request #477 from MaxUlysse/scratchInContainers
Add /scratch in containers
2 parents e0346a3 + e2bea51 commit 42f6ee1

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33 files changed

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lines changed

‎README.md‎

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@@ -1,4 +1,4 @@
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[![](doc/images/CAW_logo.png "CAW")][caw-site-link]
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[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/CAW_logo.png "CAW")][caw-site-link]
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# Cancer Analysis Workflow
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@@ -58,9 +58,9 @@ For further information/help contact: maxime.garcia@scilifelab.se, szilveszter.j
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--------------------------------------------------------------------------------
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[![](doc/images/SciLifeLab_logo.png "SciLifeLab")][scilifelab-link]
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[![](doc/images/NGI_logo.png "NGI")][ngi-link]
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[![](doc/images/NBIS_logo.png "NBIS")][nbis-link]
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[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/SciLifeLab_logo.png "SciLifeLab")][scilifelab-link]
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[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/NGI_logo.png "NGI")][ngi-link]
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[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/NBIS_logo.png "NBIS")][nbis-link]
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[ascat-link]: https://github.com/Crick-CancerGenomics/ascat
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[caw-site-link]: http://opensource.scilifelab.se/projects/caw/

‎buildContainers.nf‎

Lines changed: 19 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -36,9 +36,23 @@ kate: syntax groovy; space-indent on; indent-width 2;
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================================================================================
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*/
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39-
version = '1.2'
39+
version = '1.2.1'
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41+
// Check that Nextflow version is up to date enough
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// try / throw / catch works for NF versions < 0.25 when this was implemented
43+
nf_required_version = '0.25.0'
44+
try {
45+
if( ! nextflow.version.matches(">= $nf_required_version") ){
46+
throw GroovyException('Nextflow version too old')
47+
}
48+
} catch (all) {
49+
log.error "====================================================\n" +
50+
" Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\n" +
51+
" Pipeline execution will continue, but things may break.\n" +
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" Please update Nextflow.\n" +
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"============================================================"
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}
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41-
if (!nextflow.version.matches('>= 0.25.0')) exit 1, "Nextflow version 0.25.0 or greater is needed to run this workflow"
4256
if (params.help) exit 0, helpMessage()
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if (params.version) exit 0, versionMessage()
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if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"
@@ -222,9 +236,8 @@ def defineContainersList(){
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'mutect1',
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'picard',
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'qualimap',
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'r-base',
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'runallelecount',
226-
'runascat',
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'runconvertallelecounts',
228241
'snpeff',
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'snpeffgrch37',
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'snpeffgrch38',
@@ -253,9 +266,8 @@ def helpMessage() {
253266
log.info " Default: all"
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log.info " Possible values:"
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log.info " all, caw, fastqc, freebayes, gatk, igvtools, multiqc"
256-
log.info " mutect1, picard, qualimap, runallelecount, runascat"
257-
log.info " runconvertallelecounts, snpeff, snpeffgrch37, snpeffgrch38"
258-
log.info " vep, vepgrch37, vepgrch38"
269+
log.info " mutect1, picard, qualimap, r-base, runallelecount"
270+
log.info " snpeff, snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
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log.info " --docker: Build containers using Docker"
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log.info " --help"
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log.info " you're reading it"

‎buildReferences.nf‎

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@@ -39,9 +39,23 @@ kate: syntax groovy; space-indent on; indent-width 2;
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================================================================================
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*/
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42-
version = '1.2'
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version = '1.2.1'
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44+
// Check that Nextflow version is up to date enough
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// try / throw / catch works for NF versions < 0.25 when this was implemented
46+
nf_required_version = '0.25.0'
47+
try {
48+
if( ! nextflow.version.matches(">= $nf_required_version") ){
49+
throw GroovyException('Nextflow version too old')
50+
}
51+
} catch (all) {
52+
log.error "====================================================\n" +
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" Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\n" +
54+
" Pipeline execution will continue, but things may break.\n" +
55+
" Please update Nextflow.\n" +
56+
"============================================================"
57+
}
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44-
if (!nextflow.version.matches('>= 0.25.0')) exit 1, "Nextflow version 0.25.0 or greater is needed to run this workflow"
4559
if (params.help) exit 0, helpMessage()
4660
if (params.version) exit 0, versionMessage()
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if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"

‎configuration/docker.config‎

Lines changed: 31 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -15,35 +15,35 @@ docker {
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}
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process {
18-
$BuildBWAindexes.container = 'maxulysse/caw:1.2'
19-
$BuildPicardIndex.container = 'maxulysse/picard:1.2'
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$BuildSAMToolsIndex.container = 'maxulysse/caw:1.2'
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$BuildVCFIndex.container = 'maxulysse/igvtools:1.2'
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$ConcatVCF.container = 'maxulysse/caw:1.2'
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$CreateRecalibrationTable.container = 'maxulysse/gatk:1.2'
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$IndelRealigner.container = 'maxulysse/gatk:1.2'
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$MapReads.container = 'maxulysse/caw:1.2'
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$MarkDuplicates.container = 'maxulysse/picard:1.2'
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$MergeBams.container = 'maxulysse/caw:1.2'
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$RealignerTargetCreator.container = 'maxulysse/gatk:1.2'
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$RecalibrateBam.container = 'maxulysse/gatk:1.2'
30-
$RunAlleleCount.container = 'maxulysse/runallelecount:1.2'
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$RunAscat.container = 'maxulysse/runascat:1.2'
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$RunBamQC.container = 'maxulysse/qualimap:1.2'
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$RunBcftoolsStats.container = 'maxulysse/caw:1.2'
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$RunConvertAlleleCounts.container = 'maxulysse/runconvertallelecounts:1.2'
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$RunFastQC.container = 'maxulysse/fastqc:1.2'
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$RunFreeBayes.container = 'maxulysse/freebayes:1.2'
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$RunGenotypeGVCFs.container = 'maxulysse/gatk:1.2'
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$RunHaplotypecaller.container = 'maxulysse/gatk:1.2'
39-
$RunManta.container = 'maxulysse/caw:1.2'
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$RunMultiQC.container = 'maxulysse/multiqc:1.2'
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$RunMutect1.container = 'maxulysse/mutect1:1.2'
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$RunMutect2.container = 'maxulysse/gatk:1.2'
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$RunSamtoolsStats.container = 'maxulysse/caw:1.2'
44-
$RunSingleManta.container = 'maxulysse/caw:1.2'
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$RunSingleStrelka.container = 'maxulysse/caw:1.2'
46-
$RunSnpeff.container = {params.genome == "GRCh38" ? 'maxulysse/snpeffgrch38:1.2' : 'maxulysse/snpeffgrch37:1.2'}
47-
$RunStrelka.container = 'maxulysse/caw:1.2'
48-
$RunVEP.container = {params.genome == "GRCh38" ? 'maxulysse/vepgrch38:1.2' : 'maxulysse/vepgrch37:1.2'}
18+
$BuildBWAindexes.container = 'maxulysse/caw:1.2.1'
19+
$BuildPicardIndex.container = 'maxulysse/picard:1.2.1'
20+
$BuildSAMToolsIndex.container = 'maxulysse/caw:1.2.1'
21+
$BuildVCFIndex.container = 'maxulysse/igvtools:1.2.1'
22+
$ConcatVCF.container = 'maxulysse/caw:1.2.1'
23+
$CreateRecalibrationTable.container = 'maxulysse/gatk:1.2.1'
24+
$IndelRealigner.container = 'maxulysse/gatk:1.2.1'
25+
$MapReads.container = 'maxulysse/caw:1.2.1'
26+
$MarkDuplicates.container = 'maxulysse/picard:1.2.1'
27+
$MergeBams.container = 'maxulysse/caw:1.2.1'
28+
$RealignerTargetCreator.container = 'maxulysse/gatk:1.2.1'
29+
$RecalibrateBam.container = 'maxulysse/gatk:1.2.1'
30+
$RunAlleleCount.container = 'maxulysse/runallelecount:1.2.1'
31+
$RunAscat.container = 'maxulysse/r-base:1.2.1'
32+
$RunBamQC.container = 'maxulysse/qualimap:1.2.1'
33+
$RunBcftoolsStats.container = 'maxulysse/caw:1.2.1'
34+
$RunConvertAlleleCounts.container = 'maxulysse/r-base:1.2.1'
35+
$RunFastQC.container = 'maxulysse/fastqc:1.2.1'
36+
$RunFreeBayes.container = 'maxulysse/freebayes:1.2.1'
37+
$RunGenotypeGVCFs.container = 'maxulysse/gatk:1.2.1'
38+
$RunHaplotypecaller.container = 'maxulysse/gatk:1.2.1'
39+
$RunManta.container = 'maxulysse/caw:1.2.1'
40+
$RunMultiQC.container = 'maxulysse/multiqc:1.2.1'
41+
$RunMutect1.container = 'maxulysse/mutect1:1.2.1'
42+
$RunMutect2.container = 'maxulysse/gatk:1.2.1'
43+
$RunSamtoolsStats.container = 'maxulysse/caw:1.2.1'
44+
$RunSingleManta.container = 'maxulysse/caw:1.2.1'
45+
$RunSingleStrelka.container = 'maxulysse/caw:1.2.1'
46+
$RunSnpeff.container = {params.genome == "GRCh38" ? 'maxulysse/snpeffgrch38:1.2.1' : 'maxulysse/snpeffgrch37:1.2.1'}
47+
$RunStrelka.container = 'maxulysse/caw:1.2.1'
48+
$RunVEP.container = {params.genome == "GRCh38" ? 'maxulysse/vepgrch38:1.2.1' : 'maxulysse/vepgrch37:1.2.1'}
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}

‎configuration/singularity-path.config‎

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Original file line numberDiff line numberDiff line change
@@ -15,36 +15,36 @@ singularity {
1515
}
1616

1717
process {
18-
$BuildBWAindexes.container = 'containers/caw-1.2.img'
19-
$BuildPicardIndex.container = 'containers/picard-1.2.img'
20-
$BuildSAMToolsIndex.container = 'containers/caw-1.2.img'
21-
$BuildVCFIndex.container = 'containers/igvtools-1.2.img'
22-
$ConcatVCF.container = 'containers/caw-1.2.img'
23-
$CreateRecalibrationTable.container = 'containers/gatk-1.2.img'
24-
$GenerateMultiQCconfig.container = 'containers/multiqc-1.2.img'
25-
$IndelRealigner.container = 'containers/gatk-1.2.img'
26-
$MapReads.container = 'containers/caw-1.2.img'
27-
$MarkDuplicates.container = 'containers/picard-1.2.img'
28-
$MergeBams.container = 'containers/caw-1.2.img'
29-
$RealignerTargetCreator.container = 'containers/gatk-1.2.img'
30-
$RecalibrateBam.container = 'containers/gatk-1.2.img'
31-
$RunAlleleCount.container = 'containers/runallelecount-1.2.img'
32-
$RunAscat.container = 'containers/runascat-1.2.img'
33-
$RunBamQC.container = 'containers/qualimap-1.2.img'
34-
$RunBcftoolsStats.container = 'containers/caw-1.2.img'
35-
$RunConvertAlleleCounts.container = 'containers/runconvertallelecounts-1.2.img'
36-
$RunFastQC.container = 'containers/fastqc-1.2.img'
37-
$RunFreeBayes.container = 'containers/freebayes-1.2.img'
38-
$RunGenotypeGVCFs.container = 'containers/gatk-1.2.img'
39-
$RunHaplotypecaller.container = 'containers/gatk-1.2.img'
40-
$RunManta.container = 'containers/caw-1.2.img'
41-
$RunMultiQC.container = 'containers/multiqc-1.2.img'
42-
$RunMutect1.container = 'containers/mutect1-1.2.img'
43-
$RunMutect2.container = 'containers/gatk-1.2.img'
44-
$RunSamtoolsStats.container = 'containers/caw-1.2.img'
45-
$RunSingleManta.container = 'containers/caw-1.2.img'
46-
$RunSingleStrelka.container = 'containers/caw-1.2.img'
47-
$RunSnpeff.container = {params.genome == "GRCh38" ? 'containers/snpeffgrch38-1.2.img' : 'containers/snpeffgrch37-1.2.img'}
48-
$RunStrelka.container = 'containers/caw-1.2.img'
49-
$RunVEP.container = {params.genome == "GRCh38" ? 'containers/vepgrch38-1.2.img' : 'containers/vepgrch37-1.2.img'}
18+
$BuildBWAindexes.container = 'containers/caw-1.2.1.img'
19+
$BuildPicardIndex.container = 'containers/picard-1.2.1.img'
20+
$BuildSAMToolsIndex.container = 'containers/caw-1.2.1.img'
21+
$BuildVCFIndex.container = 'containers/igvtools-1.2.1.img'
22+
$ConcatVCF.container = 'containers/caw-1.2.1.img'
23+
$CreateRecalibrationTable.container = 'containers/gatk-1.2.1.img'
24+
$GenerateMultiQCconfig.container = 'containers/multiqc-1.2.1.img'
25+
$IndelRealigner.container = 'containers/gatk-1.2.1.img'
26+
$MapReads.container = 'containers/caw-1.2.1.img'
27+
$MarkDuplicates.container = 'containers/picard-1.2.1.img'
28+
$MergeBams.container = 'containers/caw-1.2.1.img'
29+
$RealignerTargetCreator.container = 'containers/gatk-1.2.1.img'
30+
$RecalibrateBam.container = 'containers/gatk-1.2.1.img'
31+
$RunAlleleCount.container = 'containers/runallelecount-1.2.1.img'
32+
$RunAscat.container = 'containers/r-base-1.2.1.img'
33+
$RunBamQC.container = 'containers/qualimap-1.2.1.img'
34+
$RunBcftoolsStats.container = 'containers/caw-1.2.1.img'
35+
$RunConvertAlleleCounts.container = 'containers/r-base-1.2.1.img'
36+
$RunFastQC.container = 'containers/fastqc-1.2.1.img'
37+
$RunFreeBayes.container = 'containers/freebayes-1.2.1.img'
38+
$RunGenotypeGVCFs.container = 'containers/gatk-1.2.1.img'
39+
$RunHaplotypecaller.container = 'containers/gatk-1.2.1.img'
40+
$RunManta.container = 'containers/caw-1.2.1.img'
41+
$RunMultiQC.container = 'containers/multiqc-1.2.1.img'
42+
$RunMutect1.container = 'containers/mutect1-1.2.1.img'
43+
$RunMutect2.container = 'containers/gatk-1.2.1.img'
44+
$RunSamtoolsStats.container = 'containers/caw-1.2.1.img'
45+
$RunSingleManta.container = 'containers/caw-1.2.1.img'
46+
$RunSingleStrelka.container = 'containers/caw-1.2.1.img'
47+
$RunSnpeff.container = {params.genome == "GRCh38" ? 'containers/snpeffgrch38-1.2.1.img' : 'containers/snpeffgrch37-1.2.1.img'}
48+
$RunStrelka.container = 'containers/caw-1.2.1.img'
49+
$RunVEP.container = {params.genome == "GRCh38" ? 'containers/vepgrch38-1.2.1.img' : 'containers/vepgrch37-1.2.1.img'}
5050
}

‎configuration/singularity.config‎

Lines changed: 31 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -14,35 +14,35 @@ singularity {
1414
}
1515

1616
process {
17-
$BuildBWAindexes.container = 'docker://maxulysse/caw:1.2'
18-
$BuildPicardIndex.container = 'docker://maxulysse/picard:1.2'
19-
$BuildSAMToolsIndex.container = 'docker://maxulysse/caw:1.2'
20-
$BuildVCFIndex.container = 'docker://maxulysse/igvtools:1.2'
21-
$ConcatVCF.container = 'docker://maxulysse/caw:1.2'
22-
$CreateRecalibrationTable.container = 'docker://maxulysse/gatk:1.2'
23-
$IndelRealigner.container = 'docker://maxulysse/gatk:1.2'
24-
$MapReads.container = 'docker://maxulysse/caw:1.2'
25-
$MarkDuplicates.container = 'docker://maxulysse/picard:1.2'
26-
$MergeBams.container = 'docker://maxulysse/caw:1.2'
27-
$RealignerTargetCreator.container = 'docker://maxulysse/gatk:1.2'
28-
$RecalibrateBam.container = 'docker://maxulysse/gatk:1.2'
29-
$RunAlleleCount.container = 'docker://maxulysse/runallelecount:1.2'
30-
$RunAscat.container = 'docker://maxulysse/runascat:1.2'
31-
$RunBamQC.container = 'docker://maxulysse/qualimap:1.2'
32-
$RunBcftoolsStats.container = 'docker://maxulysse/caw:1.2'
33-
$RunConvertAlleleCounts.container = 'docker://maxulysse/runconvertallelecounts:1.2'
34-
$RunFastQC.container = 'docker://maxulysse/fastqc:1.2'
35-
$RunFreeBayes.container = 'docker://maxulysse/freebayes:1.2'
36-
$RunGenotypeGVCFs.container = 'docker://maxulysse/gatk:1.2'
37-
$RunHaplotypecaller.container = 'docker://maxulysse/gatk:1.2'
38-
$RunManta.container = 'docker://maxulysse/caw:1.2'
39-
$RunMultiQC.container = 'docker://maxulysse/multiqc:1.2'
40-
$RunMutect1.container = 'docker://maxulysse/mutect1:1.2'
41-
$RunMutect2.container = 'docker://maxulysse/gatk:1.2'
42-
$RunSamtoolsStats.container = 'docker://maxulysse/caw:1.2'
43-
$RunSingleManta.container = 'docker://maxulysse/caw:1.2'
44-
$RunSingleStrelka.container = 'docker://maxulysse/caw:1.2'
45-
$RunSnpeff.container = {params.genome == "GRCh38" ? 'docker://maxulysse/snpeffgrch38:1.2' : 'docker://maxulysse/snpeffgrch37:1.2'}
46-
$RunStrelka.container = 'docker://maxulysse/caw:1.2'
47-
$RunVEP.container = {params.genome == "GRCh38" ? 'docker://maxulysse/vepgrch38:1.2' : 'docker://maxulysse/vepgrch37:1.2'}
17+
$BuildBWAindexes.container = 'docker://maxulysse/caw:1.2.1'
18+
$BuildPicardIndex.container = 'docker://maxulysse/picard:1.2.1'
19+
$BuildSAMToolsIndex.container = 'docker://maxulysse/caw:1.2.1'
20+
$BuildVCFIndex.container = 'docker://maxulysse/igvtools:1.2.1'
21+
$ConcatVCF.container = 'docker://maxulysse/caw:1.2.1'
22+
$CreateRecalibrationTable.container = 'docker://maxulysse/gatk:1.2.1'
23+
$IndelRealigner.container = 'docker://maxulysse/gatk:1.2.1'
24+
$MapReads.container = 'docker://maxulysse/caw:1.2.1'
25+
$MarkDuplicates.container = 'docker://maxulysse/picard:1.2.1'
26+
$MergeBams.container = 'docker://maxulysse/caw:1.2.1'
27+
$RealignerTargetCreator.container = 'docker://maxulysse/gatk:1.2.1'
28+
$RecalibrateBam.container = 'docker://maxulysse/gatk:1.2.1'
29+
$RunAlleleCount.container = 'docker://maxulysse/runallelecount:1.2.1'
30+
$RunAscat.container = 'docker://maxulysse/r-base:1.2.1'
31+
$RunBamQC.container = 'docker://maxulysse/qualimap:1.2.1'
32+
$RunBcftoolsStats.container = 'docker://maxulysse/caw:1.2.1'
33+
$RunConvertAlleleCounts.container = 'docker://maxulysse/r-base:1.2.1'
34+
$RunFastQC.container = 'docker://maxulysse/fastqc:1.2.1'
35+
$RunFreeBayes.container = 'docker://maxulysse/freebayes:1.2.1'
36+
$RunGenotypeGVCFs.container = 'docker://maxulysse/gatk:1.2.1'
37+
$RunHaplotypecaller.container = 'docker://maxulysse/gatk:1.2.1'
38+
$RunManta.container = 'docker://maxulysse/caw:1.2.1'
39+
$RunMultiQC.container = 'docker://maxulysse/multiqc:1.2.1'
40+
$RunMutect1.container = 'docker://maxulysse/mutect1:1.2.1'
41+
$RunMutect2.container = 'docker://maxulysse/gatk:1.2.1'
42+
$RunSamtoolsStats.container = 'docker://maxulysse/caw:1.2.1'
43+
$RunSingleManta.container = 'docker://maxulysse/caw:1.2.1'
44+
$RunSingleStrelka.container = 'docker://maxulysse/caw:1.2.1'
45+
$RunSnpeff.container = {params.genome == "GRCh38" ? 'docker://maxulysse/snpeffgrch38:1.2.1' : 'docker://maxulysse/snpeffgrch37:1.2.1'}
46+
$RunStrelka.container = 'docker://maxulysse/caw:1.2.1'
47+
$RunVEP.container = {params.genome == "GRCh38" ? 'docker://maxulysse/vepgrch38:1.2.1' : 'docker://maxulysse/vepgrch37:1.2.1'}
4848
}

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