diff --git a/gatk.wdl b/gatk.wdl
index 75e45e5904f7f30447ffb0c579988c028e9dadc9..3d4bf9231de1cc4259e10ca1c9ba9cebc34ae4e6 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -142,8 +142,8 @@ task CombineGVCFs {
-V ~{sep=' -V ' gvcfFiles} \
-L ~{sep=' -L ' intervals}
else # TODO this should be handeled in wdl
- ln -sf ~{select_first(gvcfFiles)} ~{outputPath}
- ln -sf ~{select_first(gvcfFileIndexes)} ~{outputPath}.tbi
+ ln -sf ~{gvcfFiles[0]} ~{outputPath}
+ ln -sf ~{gvcfFileIndexes[0]} ~{outputPath}.tbi
fi
}
@@ -298,7 +298,7 @@ task MuTect2 {
String? preCommand
Array[File]+ inputBams
- File inputBamIndex
+ Array[File]+ inputBamIndex
File refFasta
File refFastaIndex
File refDict
@@ -331,6 +331,7 @@ task MuTect2 {
output {
File vcfFile = outputVcf
+ File vcfIndex = outputVcf + ".tbi"
}
runtime {
diff --git a/manta.wdl b/manta.wdl
new file mode 100644
index 0000000000000000000000000000000000000000..e2c59eb425722347de5608297adc43af3cb61185
--- /dev/null
+++ b/manta.wdl
@@ -0,0 +1,63 @@
+version 1.0
+
+task Somatic {
+ input {
+ File tumorBam
+ File tumorIndex
+ File? normalBam
+ File? normalIndex
+ File refFasta
+ File refFastaIndex
+ String runDir
+ File? callRegions
+ File? callRegionsIndex
+ Boolean exome = false
+ String? preCommand
+ String? installDir
+
+ Int cores = 1
+ Int memory = 4
+ }
+
+ String toolCommand = if defined(installDir)
+ then installDir + "bin/configMata.py"
+ else "configManta.py"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ ~{"--normalBam " + normalBam} \
+ ~{"--tumorBam " + tumorBam} \
+ --referenceFasta ~{refFasta} \
+ ~{"--callRegions " + callRegions} \
+ --runDir ~{runDir} \
+ ~{true="--exome" false="" exome}
+
+ ~{runDir}/runWorkflow.py \
+ -m local \
+ -j ~{cores} \
+ -g ~{memory}
+ }
+
+ 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 defined(normalBam)
+ then runDir + "/results/variants/somaticSV.vcf.gz"
+ else runDir + "/results/variants/tumorSV.vcf.gz"
+ File tumorSVindex = if defined(normalBam)
+ 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"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ }
+}
\ No newline at end of file
diff --git a/picard.wdl b/picard.wdl
index ac372b1f078f61d2d3fdcee727fefb63dc789295..4132754149ebcab5e777f2e9d90c4266cc38db4e 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -378,3 +378,38 @@ task ScatterIntervalList {
memory: ceil(memory * memoryMultiplier)
}
}
+
+task SortVcf {
+ input {
+ String? preCommand
+ String? picardJar
+
+ Array[File]+ vcfFiles
+ String outputVcf
+
+ Int memory = 4
+ Float memoryMultiplier = 3.0
+ }
+
+ String toolCommand = if defined(picardJar)
+ then "java -Xmx" + memory + "G -jar " + picardJar
+ else "picard -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ SortVcf \
+ I=~{sep=" I=" vcfFiles} \
+ O=outputVcf
+ }
+
+ output {
+ File vcfFile = outputVcf
+ File vcfIndex = outputVcf + ".tbi"
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
\ No newline at end of file
diff --git a/samtools.wdl b/samtools.wdl
index 2d910379db88bb9402df50c2e0704e08263a9ff7..58bdcfd85b61264990af124e847a76faceefffef 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -1,5 +1,25 @@
version 1.0
+task BgzipAndIndex {
+ input {
+ File inputFile
+ String outputDir
+ String type = "vcf"
+ }
+
+ String outputGz = outputDir + "/" + basename(inputFile) + ".gz"
+
+ command {
+ bgzip -c ~{inputFile} > ~{outputGz}
+ tabix ~{outputGz} -p ~{type}
+ }
+
+ output {
+ File compressed = outputGz
+ File index = outputGz + ".tbi"
+ }
+}
+
task Index {
input {
String? preCommand
@@ -131,6 +151,21 @@ task Fastq {
}
}
+task Tabix {
+ input {
+ String inputFile
+ String type = "vcf"
+ }
+
+ command {
+ tabix ~{inputFile} -p ~{type}
+ }
+
+ output {
+ File index = inputFile + ".tbi"
+ }
+}
+
task View {
input {
String? preCommand
@@ -157,7 +192,7 @@ task View {
~{"-f " + includeFilter} \
~{"-F " + excludeFilter} \
~{"-G " + excludeSpecificFilter} \
- ~{"--threads " + threads - 1} \
+ ~{"--threads " + (threads - 1)} \
~{inFile}
}
diff --git a/strelka.wdl b/strelka.wdl
index 29e2a078ef59390d1dfceef3b093b25c0ea32236..cc3682fffeb6bfe8c9fa5241ff04d9670cb118cc 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -1,13 +1,72 @@
version 1.0
+task Germline {
+ input {
+ String? preCommand
+ String? installDir
+ String runDir
+ Array[File]+ bams
+ Array[File]+ indexes
+ File refFasta
+ File refFastaIndex
+ File? callRegions
+ File? callRegionsIndex
+ Boolean exome = false
+ Boolean rna = false
+
+ Int cores = 1
+ Int memory = 4
+ }
+
+ String toolCommand = if defined(installDir)
+ then installDir + "bin/configureStrelkaGermlineWorkflow.py"
+ else "configureStrelkaGermlineWorkflow.py"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ --bam ~{sep=" --bam " bams} \
+ --ref ~{refFasta} \
+ --runDir ~{runDir} \
+ ~{"--callRegions " + callRegions} \
+ ~{true="--exome" false="" exome} \
+ ~{true="--rna" false="" rna}
+
+ ~{runDir}/runWorkflow.py \
+ -m local \
+ -j ~{cores} \
+ -g ~{memory}
+ }
+
+ output {
+ File variants = runDir + "/results/variants/variants.vcf.gz"
+ File variantsIndex = runDir + "/results/variants/variants.vcf.gz.tbi"
+ }
+
+ runtime {
+ cpu: cores
+ memory: memory
+ }
+}
+
+
task Somatic {
input {
String? preCommand
String? installDir
String runDir
File normalBam
+ File normalIndex
File tumorBam
+ File tumorIndex
File refFasta
+ File refFastaIndex
+ File? callRegions
+ File? callRegionsIndex
+ File? indelCandidates
+ File? indelCandidatesIndex
+ Boolean exome = false
Int cores = 1
Int memory = 4
@@ -24,11 +83,14 @@ task Somatic {
--normalBam ~{normalBam} \
--tumorBam ~{tumorBam} \
--ref ~{refFasta} \
- --runDir ~{runDir}
+ --runDir ~{runDir} \
+ ~{"--callRegions " + callRegions} \
+ ~{"--indelCandidates " + indelCandidates} \
+ ~{true="--exome" false="" exome} \
~{runDir}/runWorkflow.py \
-m local \
- -J ~{cores} \
+ -j ~{cores} \
-g ~{memory}
}
diff --git a/vardict.wdl b/vardict.wdl
index 9dbb0ac49471f84ad88eb2a7c003f66ef39f9be2..a421fd785abb9f5786cb0c9781f294c5525c60fd 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -3,13 +3,17 @@ version 1.0
task VarDict {
input {
String? installDir
+ Boolean useJavaVersion = true
+ String tumorSampleName
File tumorBam
- File normalBam
+ File tumorIndex
+ String? normalSampleName
+ File? normalBam
+ File? normalIndex
File refFasta
+ File refFastaIndex
File bedFile
- String tumorSampleName
- String normalSampleName
String outputVcf
Int chromosomeColumn = 1
@@ -22,7 +26,9 @@ task VarDict {
String toolCommand = if defined(installDir)
then installDir + "/VarDict"
- else "vardict"
+ else if useJavaVersion
+ then "vardict-java" #probably needs memory stuff
+ else "vardict"
command {
set -e -o pipefail
@@ -30,19 +36,21 @@ task VarDict {
~{toolCommand} \
-G ~{refFasta} \
-N ~{tumorSampleName} \
- -b "~{tumorBam}|~{normalBam}" \
+ -b "~{tumorBam}~{"|" + normalBam}" \
-c ~{chromosomeColumn} \
-S ~{startColumn} \
-E ~{endColumn} \
-g ~{geneColumn} \
~{bedFile} | \
- ~{installDir + "/"}testsomatic.R | \
- ~{installDir + "/"}var2vcf_paired.pl \
- -N "~{tumorSampleName}|~{normalSampleName}" \
- > ~{outputVcf}
+ ~{installDir + "/"}~{true="testsomatic.R" false="teststrandbias.R" defined(normalBam)} | \
+ ~{installDir + "/"}~{true="var2vcf_paired.pl"
+ false="var2vcf_valid.pl" defined(normalBam)} \
+ -N "~{tumorSampleName}~{"|" + normalSampleName}" \
+ ~{true="" false="-E" defined(normalBam)} | \
+ bgzip -c > ~{outputVcf}
}
output {
File vcfFile = outputVcf
}
-}
\ No newline at end of file
+}