diff --git a/gatk.wdl b/gatk.wdl index bf3d8313fb01bb42b0aed731b3f5b527ad0ac8ea..38c3485a07964dc1b21e9e4cb3e29a5bf7a0cf0a 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -264,6 +264,7 @@ task MuTect2 { File? panelOfNormalsIndex String? f1r2TarGz = "f1r2.tar.gz" Array[File]+ intervals + String outputStats = outputVcf + ".stats" Int memory = 4 Float memoryMultiplier = 3 @@ -290,6 +291,7 @@ task MuTect2 { File vcfFile = outputVcf File vcfFileIndex = outputVcf + ".tbi" File f1r2File = f1r2TarGz + File stats = outputStats } runtime { @@ -326,6 +328,33 @@ task LearnReadOrientationModel { } } +task MergeStats { + input { + Array[File]+ stats + + Int memory = 2 + Float memoryMultiplier = 1.5 + String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1" + } + + command { + set -e + gatk --java-options -Xmx~{memory}G \ + MergeMutectStats \ + -stats ~{sep=" -stats " stats} \ + -O "merged.stats" + } + + output { + File mergedStats = "merged.stats" + } + + runtime { + docker: dockerImage + memory: ceil(memory * memoryMultiplier) + } +} + task SplitNCigarReads { input { File inputBam