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Merge pull request #477 from MaxUlysse/scratchInContainers
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Add /scratch in containers
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@maxulysse
maxulysse authored Oct 6, 2017
2 parents e0346a3 + e2bea51 commit 42f6ee1
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Showing 33 changed files with 455 additions and 552 deletions.
8 changes: 4 additions & 4 deletions README.md
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@@ -1,4 +1,4 @@
[![](doc/images/CAW_logo.png "CAW")][caw-site-link]
[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/CAW_logo.png "CAW")][caw-site-link]

# Cancer Analysis Workflow

Expand Down Expand Up @@ -58,9 +58,9 @@ For further information/help contact: [email protected], szilveszter.j

--------------------------------------------------------------------------------

[![](doc/images/SciLifeLab_logo.png "SciLifeLab")][scilifelab-link]
[![](doc/images/NGI_logo.png "NGI")][ngi-link]
[![](doc/images/NBIS_logo.png "NBIS")][nbis-link]
[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/SciLifeLab_logo.png "SciLifeLab")][scilifelab-link]
[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/NGI_logo.png "NGI")][ngi-link]
[![](https://raw.githubusercontent.com/SciLifeLab/CAW/master/doc/images/NBIS_logo.png "NBIS")][nbis-link]

[ascat-link]: https://github.com/Crick-CancerGenomics/ascat
[caw-site-link]: http://opensource.scilifelab.se/projects/caw/
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26 changes: 19 additions & 7 deletions buildContainers.nf
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Expand Up @@ -36,9 +36,23 @@ kate: syntax groovy; space-indent on; indent-width 2;
================================================================================
*/

version = '1.2'
version = '1.2.1'

// Check that Nextflow version is up to date enough
// try / throw / catch works for NF versions < 0.25 when this was implemented
nf_required_version = '0.25.0'
try {
if( ! nextflow.version.matches(">= $nf_required_version") ){
throw GroovyException('Nextflow version too old')
}
} catch (all) {
log.error "====================================================\n" +
" Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\n" +
" Pipeline execution will continue, but things may break.\n" +
" Please update Nextflow.\n" +
"============================================================"
}

if (!nextflow.version.matches('>= 0.25.0')) exit 1, "Nextflow version 0.25.0 or greater is needed to run this workflow"
if (params.help) exit 0, helpMessage()
if (params.version) exit 0, versionMessage()
if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"
Expand Down Expand Up @@ -222,9 +236,8 @@ def defineContainersList(){
'mutect1',
'picard',
'qualimap',
'r-base',
'runallelecount',
'runascat',
'runconvertallelecounts',
'snpeff',
'snpeffgrch37',
'snpeffgrch38',
Expand Down Expand Up @@ -253,9 +266,8 @@ def helpMessage() {
log.info " Default: all"
log.info " Possible values:"
log.info " all, caw, fastqc, freebayes, gatk, igvtools, multiqc"
log.info " mutect1, picard, qualimap, runallelecount, runascat"
log.info " runconvertallelecounts, snpeff, snpeffgrch37, snpeffgrch38"
log.info " vep, vepgrch37, vepgrch38"
log.info " mutect1, picard, qualimap, r-base, runallelecount"
log.info " snpeff, snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
log.info " --docker: Build containers using Docker"
log.info " --help"
log.info " you're reading it"
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18 changes: 16 additions & 2 deletions buildReferences.nf
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Expand Up @@ -39,9 +39,23 @@ kate: syntax groovy; space-indent on; indent-width 2;
================================================================================
*/

version = '1.2'
version = '1.2.1'

// Check that Nextflow version is up to date enough
// try / throw / catch works for NF versions < 0.25 when this was implemented
nf_required_version = '0.25.0'
try {
if( ! nextflow.version.matches(">= $nf_required_version") ){
throw GroovyException('Nextflow version too old')
}
} catch (all) {
log.error "====================================================\n" +
" Nextflow version $nf_required_version required! You are running v$workflow.nextflow.version.\n" +
" Pipeline execution will continue, but things may break.\n" +
" Please update Nextflow.\n" +
"============================================================"
}

if (!nextflow.version.matches('>= 0.25.0')) exit 1, "Nextflow version 0.25.0 or greater is needed to run this workflow"
if (params.help) exit 0, helpMessage()
if (params.version) exit 0, versionMessage()
if (!isAllowedParams(params)) exit 1, "params is unknown, see --help for more information"
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62 changes: 31 additions & 31 deletions configuration/docker.config
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Expand Up @@ -15,35 +15,35 @@ docker {
}

process {
$BuildBWAindexes.container = 'maxulysse/caw:1.2'
$BuildPicardIndex.container = 'maxulysse/picard:1.2'
$BuildSAMToolsIndex.container = 'maxulysse/caw:1.2'
$BuildVCFIndex.container = 'maxulysse/igvtools:1.2'
$ConcatVCF.container = 'maxulysse/caw:1.2'
$CreateRecalibrationTable.container = 'maxulysse/gatk:1.2'
$IndelRealigner.container = 'maxulysse/gatk:1.2'
$MapReads.container = 'maxulysse/caw:1.2'
$MarkDuplicates.container = 'maxulysse/picard:1.2'
$MergeBams.container = 'maxulysse/caw:1.2'
$RealignerTargetCreator.container = 'maxulysse/gatk:1.2'
$RecalibrateBam.container = 'maxulysse/gatk:1.2'
$RunAlleleCount.container = 'maxulysse/runallelecount:1.2'
$RunAscat.container = 'maxulysse/runascat:1.2'
$RunBamQC.container = 'maxulysse/qualimap:1.2'
$RunBcftoolsStats.container = 'maxulysse/caw:1.2'
$RunConvertAlleleCounts.container = 'maxulysse/runconvertallelecounts:1.2'
$RunFastQC.container = 'maxulysse/fastqc:1.2'
$RunFreeBayes.container = 'maxulysse/freebayes:1.2'
$RunGenotypeGVCFs.container = 'maxulysse/gatk:1.2'
$RunHaplotypecaller.container = 'maxulysse/gatk:1.2'
$RunManta.container = 'maxulysse/caw:1.2'
$RunMultiQC.container = 'maxulysse/multiqc:1.2'
$RunMutect1.container = 'maxulysse/mutect1:1.2'
$RunMutect2.container = 'maxulysse/gatk:1.2'
$RunSamtoolsStats.container = 'maxulysse/caw:1.2'
$RunSingleManta.container = 'maxulysse/caw:1.2'
$RunSingleStrelka.container = 'maxulysse/caw:1.2'
$RunSnpeff.container = {params.genome == "GRCh38" ? 'maxulysse/snpeffgrch38:1.2' : 'maxulysse/snpeffgrch37:1.2'}
$RunStrelka.container = 'maxulysse/caw:1.2'
$RunVEP.container = {params.genome == "GRCh38" ? 'maxulysse/vepgrch38:1.2' : 'maxulysse/vepgrch37:1.2'}
$BuildBWAindexes.container = 'maxulysse/caw:1.2.1'
$BuildPicardIndex.container = 'maxulysse/picard:1.2.1'
$BuildSAMToolsIndex.container = 'maxulysse/caw:1.2.1'
$BuildVCFIndex.container = 'maxulysse/igvtools:1.2.1'
$ConcatVCF.container = 'maxulysse/caw:1.2.1'
$CreateRecalibrationTable.container = 'maxulysse/gatk:1.2.1'
$IndelRealigner.container = 'maxulysse/gatk:1.2.1'
$MapReads.container = 'maxulysse/caw:1.2.1'
$MarkDuplicates.container = 'maxulysse/picard:1.2.1'
$MergeBams.container = 'maxulysse/caw:1.2.1'
$RealignerTargetCreator.container = 'maxulysse/gatk:1.2.1'
$RecalibrateBam.container = 'maxulysse/gatk:1.2.1'
$RunAlleleCount.container = 'maxulysse/runallelecount:1.2.1'
$RunAscat.container = 'maxulysse/r-base:1.2.1'
$RunBamQC.container = 'maxulysse/qualimap:1.2.1'
$RunBcftoolsStats.container = 'maxulysse/caw:1.2.1'
$RunConvertAlleleCounts.container = 'maxulysse/r-base:1.2.1'
$RunFastQC.container = 'maxulysse/fastqc:1.2.1'
$RunFreeBayes.container = 'maxulysse/freebayes:1.2.1'
$RunGenotypeGVCFs.container = 'maxulysse/gatk:1.2.1'
$RunHaplotypecaller.container = 'maxulysse/gatk:1.2.1'
$RunManta.container = 'maxulysse/caw:1.2.1'
$RunMultiQC.container = 'maxulysse/multiqc:1.2.1'
$RunMutect1.container = 'maxulysse/mutect1:1.2.1'
$RunMutect2.container = 'maxulysse/gatk:1.2.1'
$RunSamtoolsStats.container = 'maxulysse/caw:1.2.1'
$RunSingleManta.container = 'maxulysse/caw:1.2.1'
$RunSingleStrelka.container = 'maxulysse/caw:1.2.1'
$RunSnpeff.container = {params.genome == "GRCh38" ? 'maxulysse/snpeffgrch38:1.2.1' : 'maxulysse/snpeffgrch37:1.2.1'}
$RunStrelka.container = 'maxulysse/caw:1.2.1'
$RunVEP.container = {params.genome == "GRCh38" ? 'maxulysse/vepgrch38:1.2.1' : 'maxulysse/vepgrch37:1.2.1'}
}
64 changes: 32 additions & 32 deletions configuration/singularity-path.config
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Expand Up @@ -15,36 +15,36 @@ singularity {
}

process {
$BuildBWAindexes.container = 'containers/caw-1.2.img'
$BuildPicardIndex.container = 'containers/picard-1.2.img'
$BuildSAMToolsIndex.container = 'containers/caw-1.2.img'
$BuildVCFIndex.container = 'containers/igvtools-1.2.img'
$ConcatVCF.container = 'containers/caw-1.2.img'
$CreateRecalibrationTable.container = 'containers/gatk-1.2.img'
$GenerateMultiQCconfig.container = 'containers/multiqc-1.2.img'
$IndelRealigner.container = 'containers/gatk-1.2.img'
$MapReads.container = 'containers/caw-1.2.img'
$MarkDuplicates.container = 'containers/picard-1.2.img'
$MergeBams.container = 'containers/caw-1.2.img'
$RealignerTargetCreator.container = 'containers/gatk-1.2.img'
$RecalibrateBam.container = 'containers/gatk-1.2.img'
$RunAlleleCount.container = 'containers/runallelecount-1.2.img'
$RunAscat.container = 'containers/runascat-1.2.img'
$RunBamQC.container = 'containers/qualimap-1.2.img'
$RunBcftoolsStats.container = 'containers/caw-1.2.img'
$RunConvertAlleleCounts.container = 'containers/runconvertallelecounts-1.2.img'
$RunFastQC.container = 'containers/fastqc-1.2.img'
$RunFreeBayes.container = 'containers/freebayes-1.2.img'
$RunGenotypeGVCFs.container = 'containers/gatk-1.2.img'
$RunHaplotypecaller.container = 'containers/gatk-1.2.img'
$RunManta.container = 'containers/caw-1.2.img'
$RunMultiQC.container = 'containers/multiqc-1.2.img'
$RunMutect1.container = 'containers/mutect1-1.2.img'
$RunMutect2.container = 'containers/gatk-1.2.img'
$RunSamtoolsStats.container = 'containers/caw-1.2.img'
$RunSingleManta.container = 'containers/caw-1.2.img'
$RunSingleStrelka.container = 'containers/caw-1.2.img'
$RunSnpeff.container = {params.genome == "GRCh38" ? 'containers/snpeffgrch38-1.2.img' : 'containers/snpeffgrch37-1.2.img'}
$RunStrelka.container = 'containers/caw-1.2.img'
$RunVEP.container = {params.genome == "GRCh38" ? 'containers/vepgrch38-1.2.img' : 'containers/vepgrch37-1.2.img'}
$BuildBWAindexes.container = 'containers/caw-1.2.1.img'
$BuildPicardIndex.container = 'containers/picard-1.2.1.img'
$BuildSAMToolsIndex.container = 'containers/caw-1.2.1.img'
$BuildVCFIndex.container = 'containers/igvtools-1.2.1.img'
$ConcatVCF.container = 'containers/caw-1.2.1.img'
$CreateRecalibrationTable.container = 'containers/gatk-1.2.1.img'
$GenerateMultiQCconfig.container = 'containers/multiqc-1.2.1.img'
$IndelRealigner.container = 'containers/gatk-1.2.1.img'
$MapReads.container = 'containers/caw-1.2.1.img'
$MarkDuplicates.container = 'containers/picard-1.2.1.img'
$MergeBams.container = 'containers/caw-1.2.1.img'
$RealignerTargetCreator.container = 'containers/gatk-1.2.1.img'
$RecalibrateBam.container = 'containers/gatk-1.2.1.img'
$RunAlleleCount.container = 'containers/runallelecount-1.2.1.img'
$RunAscat.container = 'containers/r-base-1.2.1.img'
$RunBamQC.container = 'containers/qualimap-1.2.1.img'
$RunBcftoolsStats.container = 'containers/caw-1.2.1.img'
$RunConvertAlleleCounts.container = 'containers/r-base-1.2.1.img'
$RunFastQC.container = 'containers/fastqc-1.2.1.img'
$RunFreeBayes.container = 'containers/freebayes-1.2.1.img'
$RunGenotypeGVCFs.container = 'containers/gatk-1.2.1.img'
$RunHaplotypecaller.container = 'containers/gatk-1.2.1.img'
$RunManta.container = 'containers/caw-1.2.1.img'
$RunMultiQC.container = 'containers/multiqc-1.2.1.img'
$RunMutect1.container = 'containers/mutect1-1.2.1.img'
$RunMutect2.container = 'containers/gatk-1.2.1.img'
$RunSamtoolsStats.container = 'containers/caw-1.2.1.img'
$RunSingleManta.container = 'containers/caw-1.2.1.img'
$RunSingleStrelka.container = 'containers/caw-1.2.1.img'
$RunSnpeff.container = {params.genome == "GRCh38" ? 'containers/snpeffgrch38-1.2.1.img' : 'containers/snpeffgrch37-1.2.1.img'}
$RunStrelka.container = 'containers/caw-1.2.1.img'
$RunVEP.container = {params.genome == "GRCh38" ? 'containers/vepgrch38-1.2.1.img' : 'containers/vepgrch37-1.2.1.img'}
}
62 changes: 31 additions & 31 deletions configuration/singularity.config
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Expand Up @@ -14,35 +14,35 @@ singularity {
}

process {
$BuildBWAindexes.container = 'docker://maxulysse/caw:1.2'
$BuildPicardIndex.container = 'docker://maxulysse/picard:1.2'
$BuildSAMToolsIndex.container = 'docker://maxulysse/caw:1.2'
$BuildVCFIndex.container = 'docker://maxulysse/igvtools:1.2'
$ConcatVCF.container = 'docker://maxulysse/caw:1.2'
$CreateRecalibrationTable.container = 'docker://maxulysse/gatk:1.2'
$IndelRealigner.container = 'docker://maxulysse/gatk:1.2'
$MapReads.container = 'docker://maxulysse/caw:1.2'
$MarkDuplicates.container = 'docker://maxulysse/picard:1.2'
$MergeBams.container = 'docker://maxulysse/caw:1.2'
$RealignerTargetCreator.container = 'docker://maxulysse/gatk:1.2'
$RecalibrateBam.container = 'docker://maxulysse/gatk:1.2'
$RunAlleleCount.container = 'docker://maxulysse/runallelecount:1.2'
$RunAscat.container = 'docker://maxulysse/runascat:1.2'
$RunBamQC.container = 'docker://maxulysse/qualimap:1.2'
$RunBcftoolsStats.container = 'docker://maxulysse/caw:1.2'
$RunConvertAlleleCounts.container = 'docker://maxulysse/runconvertallelecounts:1.2'
$RunFastQC.container = 'docker://maxulysse/fastqc:1.2'
$RunFreeBayes.container = 'docker://maxulysse/freebayes:1.2'
$RunGenotypeGVCFs.container = 'docker://maxulysse/gatk:1.2'
$RunHaplotypecaller.container = 'docker://maxulysse/gatk:1.2'
$RunManta.container = 'docker://maxulysse/caw:1.2'
$RunMultiQC.container = 'docker://maxulysse/multiqc:1.2'
$RunMutect1.container = 'docker://maxulysse/mutect1:1.2'
$RunMutect2.container = 'docker://maxulysse/gatk:1.2'
$RunSamtoolsStats.container = 'docker://maxulysse/caw:1.2'
$RunSingleManta.container = 'docker://maxulysse/caw:1.2'
$RunSingleStrelka.container = 'docker://maxulysse/caw:1.2'
$RunSnpeff.container = {params.genome == "GRCh38" ? 'docker://maxulysse/snpeffgrch38:1.2' : 'docker://maxulysse/snpeffgrch37:1.2'}
$RunStrelka.container = 'docker://maxulysse/caw:1.2'
$RunVEP.container = {params.genome == "GRCh38" ? 'docker://maxulysse/vepgrch38:1.2' : 'docker://maxulysse/vepgrch37:1.2'}
$BuildBWAindexes.container = 'docker://maxulysse/caw:1.2.1'
$BuildPicardIndex.container = 'docker://maxulysse/picard:1.2.1'
$BuildSAMToolsIndex.container = 'docker://maxulysse/caw:1.2.1'
$BuildVCFIndex.container = 'docker://maxulysse/igvtools:1.2.1'
$ConcatVCF.container = 'docker://maxulysse/caw:1.2.1'
$CreateRecalibrationTable.container = 'docker://maxulysse/gatk:1.2.1'
$IndelRealigner.container = 'docker://maxulysse/gatk:1.2.1'
$MapReads.container = 'docker://maxulysse/caw:1.2.1'
$MarkDuplicates.container = 'docker://maxulysse/picard:1.2.1'
$MergeBams.container = 'docker://maxulysse/caw:1.2.1'
$RealignerTargetCreator.container = 'docker://maxulysse/gatk:1.2.1'
$RecalibrateBam.container = 'docker://maxulysse/gatk:1.2.1'
$RunAlleleCount.container = 'docker://maxulysse/runallelecount:1.2.1'
$RunAscat.container = 'docker://maxulysse/r-base:1.2.1'
$RunBamQC.container = 'docker://maxulysse/qualimap:1.2.1'
$RunBcftoolsStats.container = 'docker://maxulysse/caw:1.2.1'
$RunConvertAlleleCounts.container = 'docker://maxulysse/r-base:1.2.1'
$RunFastQC.container = 'docker://maxulysse/fastqc:1.2.1'
$RunFreeBayes.container = 'docker://maxulysse/freebayes:1.2.1'
$RunGenotypeGVCFs.container = 'docker://maxulysse/gatk:1.2.1'
$RunHaplotypecaller.container = 'docker://maxulysse/gatk:1.2.1'
$RunManta.container = 'docker://maxulysse/caw:1.2.1'
$RunMultiQC.container = 'docker://maxulysse/multiqc:1.2.1'
$RunMutect1.container = 'docker://maxulysse/mutect1:1.2.1'
$RunMutect2.container = 'docker://maxulysse/gatk:1.2.1'
$RunSamtoolsStats.container = 'docker://maxulysse/caw:1.2.1'
$RunSingleManta.container = 'docker://maxulysse/caw:1.2.1'
$RunSingleStrelka.container = 'docker://maxulysse/caw:1.2.1'
$RunSnpeff.container = {params.genome == "GRCh38" ? 'docker://maxulysse/snpeffgrch38:1.2.1' : 'docker://maxulysse/snpeffgrch37:1.2.1'}
$RunStrelka.container = 'docker://maxulysse/caw:1.2.1'
$RunVEP.container = {params.genome == "GRCh38" ? 'docker://maxulysse/vepgrch38:1.2.1' : 'docker://maxulysse/vepgrch37:1.2.1'}
}
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