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Add /scratch in containers #477

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merged 13 commits into from
Oct 6, 2017
Merged

Add /scratch in containers #477

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dcaec69
add /scratch to containers
maxulysse Oct 5, 2017
c570965
code polishing
maxulysse Oct 5, 2017
9af5cd6
update script and containers
maxulysse Oct 6, 2017
2964cb7
update containers
maxulysse Oct 6, 2017
56627b4
update to 1.2.1
maxulysse Oct 6, 2017
99a9fbe
fix containers
maxulysse Oct 6, 2017
1e12886
fix containers
maxulysse Oct 6, 2017
ad3c006
fix syntax
maxulysse Oct 6, 2017
4955695
fix zip file name
maxulysse Oct 6, 2017
fba63ac
fix #472
maxulysse Oct 6, 2017
2d7a76d
keep openjdk:8 as base for these two containers
maxulysse Oct 6, 2017
17f7f40
remove unused config file
maxulysse Oct 6, 2017
e2bea51
fix #473 by removing function
maxulysse Oct 6, 2017
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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/
Expand Down
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"
Expand Down
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"
Expand Down
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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