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d557d942 · ffinfo · 2e4f73df · d557d942 · d557d942 · d557d942
Commit d557d942 authored 6 years ago by ffinfo
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -5,8 +5,7 @@ import "common.wdl" as common
 task Mem {
    input {
        String? preCommand
-        File inputR1
+        FastqPair inputFastq
-        File? inputR2
        BwaIndex bwaIndex
        String outputPath
        String? readgroup
@@ -48,8 +47,8 @@ task Mem {
        bwa mem ~{"-t " + threads} \
        ~{readgroupArg} \
        ~{bwaIndex.fastaFile} \
-        ~{inputR1} \
+        ~{inputFastq.R1} \
-        ~{inputR2} \
+        ~{inputFastq.R2} \
        ~{altCommand} \
        | ~{picardCommand}
    }

--- a/cutadapt.wdl
+++ b/cutadapt.wdl
 version 1.0
+import "common.wdl"
 task Cutadapt {
    input {
-        File read1
+        FastqPair inputFastq
-        File? read2
        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} \
+        ~{inputFastq.R1} \
-        ~{read2} \
+        ~{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

--- a/htseq.wdl
+++ b/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}
    }

--- a/macs2.wdl
+++ b/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}

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

--- a/samtools.wdl
+++ b/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)
+        IndexedBamFile outputBam = object {
-            then select_first([bamIndexPath])
+          file: bamFilePath,
-            else bamFilePath + ".bai"
+          index: if defined(bamIndexPath)
+                              then select_first([bamIndexPath])
+                              else bamFilePath + ".bai"
+        }
    }
 }

--- a/stringtie.wdl
+++ b/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 {

--- a/vardict.wdl
+++ b/vardict.wdl
 version 1.0
+import "common.wdl"
 task VarDict {
    input {
        String? installDir
        Boolean useJavaVersion = true
        String tumorSampleName
-        File tumorBam
+        IndexedBamFile tumorBam
-        File tumorIndex
        String? normalSampleName
-        File? normalBam
+        IndexedBamFile? normalBam
-        File? normalIndex
+        Reference reference
-        File refFasta
-        File refFastaIndex
        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 {