diff --git a/strelka.wdl b/strelka.wdl new file mode 100644 index 0000000000000000000000000000000000000000..137efe9cd8e1b956a4c0a6df765c0a3fa1ea9f22 --- /dev/null +++ b/strelka.wdl @@ -0,0 +1,47 @@ +version 1.0 + +task Somatic { + input { + String? preCommand + String? installDir + String runDir + File normalBam + File tumorBam + File refFasta + + 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} + + ~{runDir}/runWorkflow.py \ + -m local \ + -J ~{cores} \ + -g ~{memory} + } + + output { + String runDir = runDir + 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 + } +} \ No newline at end of file