Merge pull request #617 from MaxUlysse/ReplaceDepreciatedSyntax

replace old depreciated syntax with withName
SciLifeLab · Aug 16, 2018 · 4517f57 · 4517f57
2 parents 375ba35 + 293c610
commit 4517f57
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -46,6 +46,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#607](https://github.com/SciLifeLab/Sarek/pull/607) - One container approach
 - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
 - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
+- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace depreciated $name syntax with withName
 
 ### `Fixed`
 - [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath`

diff --git a/configuration/containers.config b/configuration/containers.config
@@ -8,49 +8,139 @@
  */
 
 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}"}
+  }
 }
diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config
@@ -13,51 +13,145 @@ 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"}
+  }
 }