diff --git a/gatk.wdl b/gatk.wdl index 578765bd2cdba21593da9b49819d2c5664e99613..bf3d8313fb01bb42b0aed731b3f5b527ad0ac8ea 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -298,6 +298,34 @@ task MuTect2 { } } +task LearnReadOrientationModel { + input { + Array[File] f1r2TarGz + + Int memory = 4 + Float memoryMultiplier = 2 + String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1" + } + + command { + set -e + gatk --java-options -Xmx~{memory}G \ + LearnReadOrientationModel \ + -I ~{sep=" -I " f1r2TarGz} \ + -O "artifact-priors.tar.gz" + } + + output { + File artifactPriorTable = "artifact-priors.tar.gz" + } + + + runtime { + docker: dockerImage + memory: ceil(memory * memoryMultiplier) + } +} + task SplitNCigarReads { input { File inputBam