Switch to strucs

bwa.wdl

@@ -5,8 +5,7 @@ import "common.wdl" as common
 task Mem {
     input {
         String? preCommand
-        File inputR1
-        File? inputR2
+        FastqPair inputFastq
         BwaIndex bwaIndex
         String outputPath
         String? readgroup
@@ -48,8 +47,8 @@ task Mem {
         bwa mem ~{"-t " + threads} \
         ~{readgroupArg} \
         ~{bwaIndex.fastaFile} \
-        ~{inputR1} \
-        ~{inputR2} \
+        ~{inputFastq.R1} \
+        ~{inputFastq.R2} \
         ~{altCommand} \
         | ~{picardCommand}
     }

cutadapt.wdl

 version 1.0
 
+import "common.wdl"
+
 task Cutadapt {
     input {
-        File read1
-        File? read2
+        FastqPair inputFastq
         String read1output
         String? read2output
         String? format
@@ -119,15 +120,17 @@ task Cutadapt {
         ~{true="--bwa" false="" bwa} \
         ~{true="--zero-cap" false="" zeroCap} \
         ~{true="--no-zero-cap" false="" noZeroCap} \
-        ~{read1} \
-        ~{read2} \
+        ~{inputFastq.R1} \
+        ~{inputFastq.R2} \
         ~{"> " + reportPath}
     }
 
     output{
+        FastqPair cutOutput = object {
+          R1: read1output,
+          R2: read2output
+        }
         File report = if defined(reportPath) then select_first([reportPath]) else stdout()
-        File cutRead1 = read1output
-        File? cutRead2 = read2output
         File? tooLongOutput=tooLongOutputPath
         File? tooShortOutput=tooShortOutputPath
         File? untrimmedOutput=untrimmedOutputPath

htseq.wdl

@@ -3,7 +3,7 @@ version 1.0
 task HTSeqCount {
     input {
         String? preCommand
-        Array[File] alignmentFiles
+        Array[IndexedBamFile] inputBamFiles
         File gtfFile
         String outputTable
         String format = "bam"
@@ -21,7 +21,7 @@ task HTSeqCount {
         -f ~{format} \
         -r ~{order} \
         -s ~{stranded} \
-        ~{sep=" " alignmentFiles} \
+        ~{sep=" " inputBamFiles.file} \
         ~{gtfFile} \
         > ~{outputTable}
     }

macs2.wdl

@@ -3,7 +3,7 @@ version 1.0
 task PeakCalling {
     input {
         String? preCommand
-        Array[File] bamFiles
+        Array[IndexedBamFile] bamFiles
         String outDir
         String sampleName
         Int threads = 1
@@ -15,7 +15,7 @@ task PeakCalling {
         set -e -o pipefail
         ~{preCommand}
         macs2 callpeak \
-        --treatment ~{sep = ' ' bamFiles} \
+        --treatment ~{sep = ' ' bamFiles.file} \
         --outdir ~{outDir} \
         --name ~{sampleName} \
         ~{true='--nomodel' false='' nomodel}

manta.wdl

 version 1.0
 
+import "common.wdl"
+
 task ConfigureSomatic {
     input {
-        File tumorBam
-        File tumorIndex
-        File? normalBam
-        File? normalIndex
-        File refFasta
-        File refFastaIndex
+        IndexedBamFile tumorBam
+        IndexedBamFile? normalBam
+        Reference reference
         String runDir
         File? callRegions
         File? callRegionsIndex
@@ -24,9 +23,9 @@ task ConfigureSomatic {
         set -e -o pipefail
         ~{preCommand}
         ~{toolCommand} \
-        ~{"--normalBam " + normalBam} \
-        ~{"--tumorBam " + tumorBam} \
-        --referenceFasta ~{refFasta} \
+        ~{"--normalBam " + normalBam.file} \
+        ~{"--tumorBam " + tumorBam.file} \
+        --referenceFasta ~{reference.fasta} \
         ~{"--callRegions " + callRegions} \
         --runDir ~{runDir} \
         ~{true="--exome" false="" exome}
@@ -53,19 +52,28 @@ task RunSomatic {
     }
 
     output {
-        File condidateSmallIndels = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
-        File condidateSmallIndelsIndex = runDir +
-            "/results/variants/candidateSmallIndels.vcf.gz.tbi"
-        File candidateSV = runDir + "/results/variants/candidateSV.vcf.gz"
-        File candidateSVindex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
-        File tumorSV = if paired
-            then runDir + "/results/variants/somaticSV.vcf.gz"
-            else runDir + "/results/variants/tumorSV.vcf.gz"
-        File tumorSVindex = if paired
-            then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
-            else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
-        File? diploidSV = "/results/variants/diploidSV.vcf.gz"
-        File? diploidSVindex = "/results/variants/diploidSV.vcf.gz.tbi"
+        IndexedVcfFile condidateSmallIndels = object {
+          file: runDir + "/results/variants/candidateSmallIndels.vcf.gz",
+          index: runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
+        }
+        IndexedVcfFile candidateSV = object {
+          file: runDir + "/results/variants/candidateSV.vcf.gz",
+          index: runDir + "/results/variants/candidateSV.vcf.gz.tbi"
+        }
+        File tumorSV = if (paired)
+            then object {
+              file: runDir + "/results/variants/somaticSV.vcf.gz",
+              index: runDir + "/results/variants/somaticSV.vcf.gz.tbi"
+            }
+            else object {
+              file: runDir + "/results/variants/tumorSV.vcf.gz",
+              index: runDir + "/results/variants/tumorSV.vcf.gz.tbi"
+            }
+
+        IndexedVcfFile diploidSV = object {
+          file: runDir + "/results/variants/diploidSV.vcf.gz",
+          index: runDir + "/results/variants/diploidSV.vcf.gz.tbi"
+        }
     }
 
     runtime {

samtools.wdl

 version 1.0
 
+import "common.wdl"
+
 task BgzipAndIndex {
     input {
         File inputFile
@@ -34,9 +36,12 @@ task Index {
     }
 
     output {
-        File indexFile = if defined(bamIndexPath)
-            then select_first([bamIndexPath])
-            else bamFilePath + ".bai"
+        IndexedBamFile outputBam = object {
+          file: bamFilePath,
+          index: if defined(bamIndexPath)
+                              then select_first([bamIndexPath])
+                              else bamFilePath + ".bai"
+        }
     }
 }
 

stringtie.wdl

@@ -3,7 +3,7 @@ version 1.0
 task Stringtie {
     input {
         String? preCommand
-        File alignedReads
+        IndexedBamFile bam
         File? referenceGtf
         Int threads = 1
         String assembledTranscriptsFile
@@ -23,7 +23,7 @@ task Stringtie {
         ~{true="fr" false="" secondStranded} \
         -o ~{assembledTranscriptsFile} \
         ~{"-A " + geneAbundanceFile} \
-        ~{alignedReads}
+        ~{bam.file}
     }
 
     output {

vardict.wdl

 version 1.0
 
+import "common.wdl"
+
 task VarDict {
     input {
         String? installDir
         Boolean useJavaVersion = true
 
         String tumorSampleName
-        File tumorBam
-        File tumorIndex
+        IndexedBamFile tumorBam
         String? normalSampleName
-        File? normalBam
-        File? normalIndex
-        File refFasta
-        File refFastaIndex
+        IndexedBamFile? normalBam
+        Reference reference
         File bedFile
         String outputVcf
 
@@ -37,9 +36,9 @@ task VarDict {
         export JAVA_OPTS="-Xmx~{memory}G"
         ~{preCommand}
         ~{toolCommand} \
-        -G ~{refFasta} \
+        -G ~{reference.fasta} \
         -N ~{tumorSampleName} \
-        -b "~{tumorBam}~{"|" + normalBam}" \
+        -b "~{tumorBam.file}~{"|" + normalBam.file}" \
         ~{true="" false="-z" defined(normalBam)} \
         -c ~{chromosomeColumn} \
         -S ~{startColumn} \
@@ -52,10 +51,14 @@ task VarDict {
         -N "~{tumorSampleName}~{"|" + normalSampleName}" \
         ~{true="" false="-E" defined(normalBam)} | \
         bgzip -c > ~{outputVcf}
+        tabix -p vcf ~{outputVcf}
     }
 
     output {
-        File vcfFile = outputVcf
+        IndexedVcfFile vcfFile = object {
+          file: outputVcf,
+          index: outputVcf + ".tbi"
+        }
     }
 
     runtime {