fix syntax

SciLifeLab · Aug 15, 2018 · 293c610 · 293c610
1 parent c989afa
commit 293c610
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diff --git a/configuration/containers.config b/configuration/containers.config
@@ -8,49 +8,139 @@
  */
 
 process {
-  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}"}
+  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 {
-  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"}
+  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"}
+  }
 }
diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
@@ -40,7 +40,7 @@ process {
 
   // These processes are defined in buildReferences.nf
 
-withName:BuildBWAindexes {
+  withName:BuildBWAindexes {
     memory = {params.totalMemory} // TODO This is likely too high
   }
   withName:BuildReferenceIndex {
@@ -55,7 +55,7 @@ withName:BuildBWAindexes {
 
   // These processes are defined in main.nf
 
-withName:ConcatVCF {
+  withName:ConcatVCF {
     cpus = 8
   }
   withName:CreateRecalibrationTable {