diff --git a/rtg.wdl b/rtg.wdl index bc2caef689878ea70e4db97b1806725cc5822f49..c528c3a1043255d9aae1c006c7713f34c7f4eb18 100644 --- a/rtg.wdl +++ b/rtg.wdl @@ -26,13 +26,14 @@ task Format { String outputPath = "seq_data.sdf" Array[File]+ inputFiles String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0" - String memory = "4G" + String rtgMem = "8G" + String memory = "16G" } command { set -e mkdir -p $(dirname ~{outputPath}) - rtg format -f ~{format} \ + rtg RTG_MEM=~{rtgMem} format -f ~{format} \ -o ~{outputPath} \ ~{sep=' ' inputFiles} } @@ -74,14 +75,15 @@ task VcfEval { Boolean squashPloidy = false String outputMode = "split" Int threads = 1 # tool default is number of cores in the system 😱 - String memory = "4G" + String rtgMem = "4G" + String memory = "8G" String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0" } command <<< set -e mkdir -p "$(dirname ~{outputDir})" - rtg vcfeval \ + rtg RTG_MEM=~{rtgMem} vcfeval \ --baseline ~{baseline} \ --calls ~{calls} \ ~{"--evaluation-regions " + evaluationRegions} \