diff --git a/CHANGELOG.md b/CHANGELOG.md index 79d6668ac833e92212fe8b239289e0b71a045164..1733c93fd5f515b08a82a9295091fa9645a8b0bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ version 5.0.0-dev --------------------------- + Bam2fastx: Input bam and index are now arrays. + Lima: Remove globs from outputs. ++ Updated task gridss.wdl: add --jvmheap parameter + A bwa-mem2 task was created with the same interface (including usePostalt) as the bwa mem task. + bwa mem and bwa kit are now one task. The usePostalt boolean can be used to diff --git a/gridss.wdl b/gridss.wdl index 3d4b7d7399c0ae759b8b5efd99bd0b6908450798..3b7859b653f93f8160ac5c79023d0480dd943f09 100644 --- a/gridss.wdl +++ b/gridss.wdl @@ -33,6 +33,7 @@ task GRIDSS { BwaIndex reference String outputPrefix = "gridss" + Int jvmHeapSizeGb = 30 Int threads = 1 String dockerImage = "quay.io/biocontainers/gridss:2.9.4--0" } @@ -45,6 +46,7 @@ task GRIDSS { --output ~{outputPrefix}.vcf.gz \ --assembly ~{outputPrefix}_assembly.bam \ ~{"-t " + threads} \ + ~{"--jvmheap " + jvmHeapSizeGb + "G"} \ --label ~{normalLabel}~{true="," false="" defined(normalLabel)}~{tumorLabel} \ ~{normalBam} \ ~{tumorBam} @@ -61,7 +63,7 @@ task GRIDSS { runtime { cpu: threads - memory: "32G" + memory: "~{jvmHeapSizeGb + 1}G" docker: dockerImage }