Merge branch 'develop' into BIOWDL-487

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

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
     }