diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl index 8199958e1ff7dcad1dc931abbcf5991c86a79070..3c7ac7b5aa56323a75089236fefe31fad791a9d4 100644 --- a/biopet/biopet.wdl +++ b/biopet/biopet.wdl @@ -251,7 +251,6 @@ task ScatterRegions { String outputDirPath = "scatters" } - command { set -e -o pipefail mkdir -p ~{outputDirPath} diff --git a/gatk.wdl b/gatk.wdl index c354c7db3b07d08b32de9b39359cfa6cb52b9f3d..8c5e42538ec4586c858181b042d109b277eb5cbb 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -96,10 +96,7 @@ task CombineGVCFs { Array[File]+ gvcfFiles Array[File]+ gvcfFilesIndex Array[File]+ intervals - String outputPath - - Reference reference Int memory = 4 @@ -166,11 +163,8 @@ task GenotypeGVCFs { Array[File]+ gvcfFiles Array[File]+ gvcfFilesIndex Array[File]+ intervals - String outputPath - Reference reference - IndexedVcfFile? dbsnpVCF Int memory = 6 @@ -217,7 +211,6 @@ task HaplotypeCallerGvcf { String gvcfPath Reference reference Float contamination = 0.0 - IndexedVcfFile? dbsnpVCF Int memory = 4