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task Germline {
input {
String? preCommand
String? installDir
String runDir
Array[File]+ bams
Array[File]+ indexes
File refFasta
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.vcf.gz"
File variantsIndex = runDir + "/results/variants.vcf.gz.tbi"
}
runtime {
cpu: cores
memory: memory
}
}
task Somatic {
input {
String? preCommand
String? installDir
String runDir
File normalBam
File? callRegions
File? callRegionsIndex
Boolean exome = false
Int cores = 1
Int memory = 4
}
String toolCommand = if defined(installDir)
then installDir + "bin/configureStrelkaSomaticWorkflow.py"
else "configureStrelkaSomaticWorkflow.py"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
--normalBam ~{normalBam} \
--tumorBam ~{tumorBam} \
--ref ~{refFasta} \
--runDir ~{runDir} \
~{"--callRegions" + callRegions} \
~{true="--exome" false="" exome} \
~{runDir}/runWorkflow.py \
-m local \
-J ~{cores} \
-g ~{memory}
}
output {
File indelsVcf = runDir + "/results/variants/somatic.indels.vcf.gz"
File indelsIndex = runDir + "/results/variants/somatic.indels.vcf.gz.tbi"
File snvVcf = runDir + "/results/variants/somatic.snvs.vcf.gz"
File snvIndex = runDir + "/results/variants/somatic.snvs.vcf.gz.tbi"
}
runtime {
cpu: cores
memory: memory
}
}