diff --git a/manta.wdl b/manta.wdl
index 6eb724844b28ce44b1b1f7f2120659058501470c..546d468c166fa75a615b63e836aa83a76f316f6e 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -4,10 +4,13 @@ import "common.wdl"
task Somatic {
input {
- IndexedBamFile tumorBam
- IndexedBamFile? normalBam
- Reference reference
- String runDir
+ File tumorBam
+ File tumorBamIndex
+ File? normalBam
+ File? normalBamIndex
+ File referenceFasta
+ File referenceFastaFai
+ String runDir = "."
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -16,19 +19,15 @@ task Somatic {
Int memory = 4
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
- File? doNotDefineThis #FIXME
}
- File? normalBamFile = if defined(normalBam)
- then select_first([normalBam]).file
- else doNotDefineThis
-
command {
+ mkdir -p ~{runDir}
set -e
configManta.py \
- ~{"--normalBam " + normalBamFile} \
- ~{"--tumorBam " + tumorBam.file} \
- --referenceFasta ~{reference.fasta} \
+ ~{"--normalBam " + normalBam} \
+ ~{"--tumorBam " + tumorBam} \
+ --referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
@@ -40,25 +39,16 @@ task Somatic {
}
output {
- IndexedVcfFile candidateSmallIndels = 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"
- }
- IndexedVcfFile tumorSV = if defined(normalBam)
- 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"
- }
-
- #FIXME: workaround for https://github.com/broadinstitute/cromwell/issues/4111
+ File candidateSmallIndelsVcf = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
+ File candidateSmallIndelsVcfIndex = runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
+ File candidateSVVcf = runDir + "/results/variants/candidateSV.vcf.gz"
+ File candidatSVVcfIndex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
+ File tumorSVVcf = if defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz"
+ else runDir + "/results/variants/tumorSV.vcf.gz"
+ File tumorSVVcfIndex = if defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
+ else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
File? diploidSV = runDir + "/results/variants/diploidSV.vcf.gz"
File? diploidSVindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
diff --git a/samtools.wdl b/samtools.wdl
index e83474be6b805829cdb91b7b35ff64d225d16091..45376a09fecaf1ee28bf3ba70555933f1c40a2eb 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -13,6 +13,7 @@ task BgzipAndIndex {
command {
set -e
+ mkdir -p $(dirname ~{outputGz})
bgzip -c ~{inputFile} > ~{outputGz}
tabix ~{outputGz} -p ~{type}
}
@@ -36,6 +37,8 @@ task Index {
}
command {
+ set -e
+ mkdir -p $(dirname ~{bamIndexPath})
samtools index ~{bamFile} ~{bamIndexPath}
}
@@ -85,6 +88,8 @@ task Markdup {
}
command {
+ set -e
+ mkdir -p $(dirname ~{outputBamPath})
samtools markdup ~{inputBam} ~{outputBamPath}
}
@@ -222,6 +227,8 @@ task View {
}
command {
+ set -e
+ mkdir -p $(dirname ~{outputFileName})
samtools view \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 9e47183f3d2f47e9d21be83883714d9c095e4298..d1163b4a1fcda41b45f9e3a12e7eb5b2ad16c882 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -1,7 +1,5 @@
version 1.0
-import "common.wdl" as common
-
task ParallelPaired {
input {
String installDir = "/opt/somaticseq" #the location in the docker image
@@ -9,11 +7,14 @@ task ParallelPaired {
File? classifierSNV
File? classifierIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile tumorBam
- IndexedBamFile normalBam
+ File tumorBam
+ File tumorBamIndex
+ File normalBam
+ File normalBamIndex
File? mutect2VCF
File? varscanSNV
File? varscanIndel
@@ -36,13 +37,13 @@ task ParallelPaired {
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
- --tumor-bam-file ~{tumorBam.file} \
- --normal-bam-file ~{normalBam.file} \
+ --tumor-bam-file ~{tumorBam} \
+ --normal-bam-file ~{normalBam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
@@ -81,11 +82,14 @@ task ParallelPairedTrain {
File truthSNV
File truthIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile tumorBam
- IndexedBamFile normalBam
+ File tumorBam
+ File tumorBamIndex
+ File normalBam
+ File normalBamIndex
File? mutect2VCF
File? varscanSNV
File? varscanIndel
@@ -109,13 +113,13 @@ task ParallelPairedTrain {
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
- --tumor-bam-file ~{tumorBam.file} \
- --normal-bam-file ~{normalBam.file} \
+ --tumor-bam-file ~{tumorBam} \
+ --normal-bam-file ~{normalBam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
@@ -152,10 +156,12 @@ task ParallelSingle {
File? classifierSNV
File? classifierIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile bam
+ File bam
+ File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
@@ -172,12 +178,12 @@ task ParallelSingle {
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
- --bam-file ~{bam.file} \
+ --bam-file ~{bam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
@@ -210,10 +216,12 @@ task ParallelSingleTrain {
File truthSNV
File truthIndel
String outputDir
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? inclusionRegion
File? exclusionRegion
- IndexedBamFile bam
+ File bam
+ File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
@@ -231,12 +239,12 @@ task ParallelSingleTrain {
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
- --genome-reference ~{reference.fasta} \
+ --genome-reference ~{referenceFasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
- --bam-file ~{bam.file} \
+ --bam-file ~{bam} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
diff --git a/strelka.wdl b/strelka.wdl
index f9166ecc928a489d94ecfcc92c062ea00370a40c..262d3fdc5a12edc75e7fb36cc4f39e16dac28141 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -4,10 +4,11 @@ import "common.wdl" as common
task Germline {
input {
- String runDir
+ String runDir = "."
Array[File]+ bams
Array[File]+ indexes
- Reference reference
+ File referenceFasta
+ File referenceFastaFai
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -20,9 +21,10 @@ task Germline {
command {
set -e
+ mkdir -p ~{runDir}
configureStrelkaGermlineWorkflow.py \
--bam ~{sep=" --bam " bams} \
- --ref ~{reference.fasta} \
+ --ref ~{referenceFasta} \
--runDir ~{runDir} \
~{"--callRegions " + callRegions} \
~{true="--exome" false="" exome} \
@@ -48,13 +50,17 @@ task Germline {
task Somatic {
input {
- String runDir
- IndexedBamFile normalBam
- IndexedBamFile tumorBam
- Reference reference
+ String runDir = "."
+ File normalBam
+ File normalBamIndex
+ File tumorBam
+ File tumorBamIndex
+ File referenceFasta
+ File referenceFastaFai
File? callRegions
File? callRegionsIndex
- IndexedVcfFile? indelCandidates
+ File? indelCandidatesVcf
+ File? indelCandidatesVcfIndex
Boolean exome = false
Int cores = 1
@@ -64,19 +70,16 @@ task Somatic {
File? doNotDefineThis #FIXME
}
- File? indelCandidatesFile = if (defined(indelCandidates))
- then select_first([indelCandidates]).file
- else doNotDefineThis
-
command {
set -e
+ mkdir -p ~{runDir}
configureStrelkaSomaticWorkflow.py \
- --normalBam ~{normalBam.file} \
- --tumorBam ~{tumorBam.file} \
- --ref ~{reference.fasta} \
+ --normalBam ~{normalBam} \
+ --tumorBam ~{tumorBam} \
+ --ref ~{referenceFasta} \
--runDir ~{runDir} \
~{"--callRegions " + callRegions} \
- ~{"--indelCandidates " + indelCandidatesFile} \
+ ~{"--indelCandidates " + indelCandidatesVcf} \
~{true="--exome" false="" exome}
~{runDir}/runWorkflow.py \
diff --git a/vardict.wdl b/vardict.wdl
index 0fe6ee14dbc40e28de5a029894ead72321e1ecac..0cbf38acd7a69f22e4b760f7f17932f585a52852 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -5,10 +5,13 @@ import "common.wdl"
task VarDict {
input {
String tumorSampleName
- IndexedBamFile tumorBam
+ File tumorBam
+ File tumorBamIndex
String? normalSampleName
- IndexedBamFile? normalBam
- Reference reference
+ File? normalBam
+ File? normalBamIndex
+ File referenceFasta
+ File referenceFastaFai
File bedFile
String outputVcf
@@ -22,21 +25,16 @@ task VarDict {
Float memoryMultiplier = 2.5
String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
- File? doNotDefineThis #FIXME
}
- File? normalBamFile = if defined(normalBam)
- then select_first([normalBam]).file
- else doNotDefineThis
-
command {
set -e -o pipefail
export JAVA_OPTS="-Xmx~{memory}G"
vardict-java \
~{"-th " + threads} \
- -G ~{reference.fasta} \
+ -G ~{referenceFasta} \
-N ~{tumorSampleName} \
- -b "~{tumorBam.file}~{"|" + normalBamFile}" \
+ -b "~{tumorBam}~{"|" + normalBam}" \
~{true="" false="-z" defined(normalBam)} \
-c ~{chromosomeColumn} \
-S ~{startColumn} \