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replace old depreciated syntax with withName: to close nf-core#600
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@maxulysse
maxulysse committed Aug 15, 2018
1 parent 924b90a commit 6a4309d
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90 changes: 45 additions & 45 deletions configuration/containers.config
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Original file line number Diff line number Diff line change
Expand Up @@ -8,49 +8,49 @@
*/

process {
$BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}"
$BuildReferenceIndex.container = "${params.repository}/sarek:${params.tag}"
$BuildSAMToolsIndex.container = "${params.repository}/sarek:${params.tag}"
$BuildVCFIndex.container = "${params.repository}/sarek:${params.tag}"
$CompressVCF.container = "${params.repository}/sarek:${params.tag}"
$ConcatVCF.container = "${params.repository}/sarek:${params.tag}"
$CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}"
$GetVersionAll.container = "${params.repository}/sarek:${params.tag}"
$GetVersionAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
$GetVersionASCAT.container = "${params.repository}/r-base:${params.tag}"
$GetVersionBamQC.container = "${params.repository}/sarek:${params.tag}"
$GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}"
$GetVersionBWAsamtools.container = "${params.repository}/sarek:${params.tag}"
$GetVersionFastQC.container = "${params.repository}/sarek:${params.tag}"
$GetVersionFreeBayes.container = "${params.repository}/sarek:${params.tag}"
$GetVersionGATK.container = "${params.repository}/sarek:${params.tag}"
$GetVersionManta.container = "${params.repository}/sarek:${params.tag}"
$GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
$GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}"
$GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}"
$GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
$MapReads.container = "${params.repository}/sarek:${params.tag}"
$MarkDuplicates.container = "${params.repository}/sarek:${params.tag}"
$MergeBams.container = "${params.repository}/sarek:${params.tag}"
$RecalibrateBam.container = "${params.repository}/sarek:${params.tag}"
$RunAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
$RunAscat.container = "${params.repository}/r-base:${params.tag}"
$RunBamQC.container = "${params.repository}/sarek:${params.tag}"
$RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}"
$RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}"
$RunFastQC.container = "${params.repository}/sarek:${params.tag}"
$RunFreeBayes.container = "${params.repository}/sarek:${params.tag}"
$RunGenotypeGVCFs.container = "${params.repository}/sarek:${params.tag}"
$RunHaplotypecaller.container = "${params.repository}/sarek:${params.tag}"
$RunManta.container = "${params.repository}/sarek:${params.tag}"
$RunMultiQC.container = "${params.repository}/sarek:${params.tag}"
$RunMutect2.container = "${params.repository}/sarek:${params.tag}"
$RunSamtoolsStats.container = "${params.repository}/sarek:${params.tag}"
$RunSingleManta.container = "${params.repository}/sarek:${params.tag}"
$RunSingleStrelka.container = "${params.repository}/sarek:${params.tag}"
$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
$RunStrelka.container = "${params.repository}/sarek:${params.tag}"
$RunStrelkaBP.container = "${params.repository}/sarek:${params.tag}"
$RunVcftools.container = "${params.repository}/sarek:${params.tag}"
$RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
withName:BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}"
withName:BuildReferenceIndex.container = "${params.repository}/sarek:${params.tag}"
withName:BuildSAMToolsIndex.container = "${params.repository}/sarek:${params.tag}"
withName:BuildVCFIndex.container = "${params.repository}/sarek:${params.tag}"
withName:CompressVCF.container = "${params.repository}/sarek:${params.tag}"
withName:ConcatVCF.container = "${params.repository}/sarek:${params.tag}"
withName:CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionAll.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
withName:GetVersionASCAT.container = "${params.repository}/r-base:${params.tag}"
withName:GetVersionBamQC.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionBWAsamtools.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionFastQC.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionFreeBayes.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionGATK.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionManta.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
withName:GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}"
withName:GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
withName:MapReads.container = "${params.repository}/sarek:${params.tag}"
withName:MarkDuplicates.container = "${params.repository}/sarek:${params.tag}"
withName:MergeBams.container = "${params.repository}/sarek:${params.tag}"
withName:RecalibrateBam.container = "${params.repository}/sarek:${params.tag}"
withName:RunAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
withName:RunAscat.container = "${params.repository}/r-base:${params.tag}"
withName:RunBamQC.container = "${params.repository}/sarek:${params.tag}"
withName:RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}"
withName:RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}"
withName:RunFastQC.container = "${params.repository}/sarek:${params.tag}"
withName:RunFreeBayes.container = "${params.repository}/sarek:${params.tag}"
withName:RunGenotypeGVCFs.container = "${params.repository}/sarek:${params.tag}"
withName:RunHaplotypecaller.container = "${params.repository}/sarek:${params.tag}"
withName:RunManta.container = "${params.repository}/sarek:${params.tag}"
withName:RunMultiQC.container = "${params.repository}/sarek:${params.tag}"
withName:RunMutect2.container = "${params.repository}/sarek:${params.tag}"
withName:RunSamtoolsStats.container = "${params.repository}/sarek:${params.tag}"
withName:RunSingleManta.container = "${params.repository}/sarek:${params.tag}"
withName:RunSingleStrelka.container = "${params.repository}/sarek:${params.tag}"
withName:RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
withName:RunStrelka.container = "${params.repository}/sarek:${params.tag}"
withName:RunStrelkaBP.container = "${params.repository}/sarek:${params.tag}"
withName:RunVcftools.container = "${params.repository}/sarek:${params.tag}"
withName:RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
}
94 changes: 47 additions & 47 deletions configuration/singularity-path.config
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Original file line number Diff line number Diff line change
Expand Up @@ -13,51 +13,51 @@ singularity {
}

process {
$BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img"
$BuildReferenceIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
$BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
$BuildVCFIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
$CompressVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
$ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
$CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionAll.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
$GetVersionASCAT.container = "${params.containerPath}/r-base-${params.tag}.img"
$GetVersionBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionGATK.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionManta.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
$GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionVCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
$IndelRealigner.container = "${params.containerPath}/sarek-${params.tag}.img"
$MapReads.container = "${params.containerPath}/sarek-${params.tag}.img"
$MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img"
$MergeBams.container = "${params.containerPath}/sarek-${params.tag}.img"
$RealignerTargetCreator.container = "${params.containerPath}/sarek-${params.tag}.img"
$RecalibrateBam.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
$RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img"
$RunBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img"
$RunFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunGenotypeGVCFs.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunHaplotypecaller.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunManta.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunMultiQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunMutect2.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSingleManta.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSingleStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
$RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunVcftools.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
withName:BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:BuildReferenceIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:BuildVCFIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:CompressVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionAll.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
withName:GetVersionASCAT.container = "${params.containerPath}/r-base-${params.tag}.img"
withName:GetVersionBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionGATK.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionManta.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
withName:GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionVCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
withName:IndelRealigner.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:MapReads.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:MergeBams.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RealignerTargetCreator.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RecalibrateBam.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
withName:RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img"
withName:RunBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img"
withName:RunFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunGenotypeGVCFs.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunHaplotypecaller.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunManta.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunMultiQC.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunMutect2.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunSingleManta.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunSingleStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
withName:RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunVcftools.container = "${params.containerPath}/sarek-${params.tag}.img"
withName:RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
}
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