diff --git a/somaticseq.wdl b/somaticseq.wdl index d1163b4a1fcda41b45f9e3a12e7eb5b2ad16c882..4a8b860d71f6e8750f482b91419fd619a21968d1 100644 --- a/somaticseq.wdl +++ b/somaticseq.wdl @@ -267,3 +267,30 @@ task ParallelSingleTrain { docker: dockerImage } } + +task ModifyStrelka { + input { + String installDir = "/opt/somaticseq/vcfModifier" #the location in the docker image + + File strelkaVCF + String? outputVCFName = basename(strelkaVCF, ".gz") + + Int threads = 1 + String dockerImage = "lethalfang/somaticseq:3.1.0" + } + + command { + ~{installDir}/modify_Strelka.py \ + -infile ~{strelkaVCF} \ + -outfile ~{outputVCFName} + } + + output { + File outputVcf = outputVCFName + } + + runtime { + cpu: threads + docker: dockerImage + } +}