diff --git a/gatk.wdl b/gatk.wdl index 59f08ce3878b3ec858da830c7f74f0f397b43eed..21543907e95db3f0136c3c06dc966decccf23ee8 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -331,8 +331,8 @@ task MergeStats { input { Array[File]+ stats - Int memory = 2 - Float memoryMultiplier = 1.5 + Int memory = 14 + Float memoryMultiplier = 2 String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1" } @@ -435,7 +435,7 @@ task FilterMutectCalls { File mutect2Stats String? extraArgs - Int memory = 4 + Int memory = 8 Float memoryMultiplier = 1.5 String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1" } @@ -558,4 +558,4 @@ task CombineVariants { docker: dockerImage memory: ceil(memory * memoryMultiplier) } -} \ No newline at end of file +} diff --git a/somaticseq.wdl b/somaticseq.wdl index 349c7d2f4b9042167990a1b26d7b7cbb18c140b3..7a25a0817950525000d53e2b13eccf4d79bfa323 100644 --- a/somaticseq.wdl +++ b/somaticseq.wdl @@ -280,7 +280,7 @@ task ModifyStrelka { } command { - set -e -o pipefail + set -e ~{installDir}/modify_Strelka.py \ -infile ~{strelkaVCF} \