diff --git a/gridss.wdl b/gridss.wdl index fcfed095e58b7a8e7c5e2dbda64f80fed15fa5b4..03193cca1dfa068a9824035037ce6da7cf66369a 100644 --- a/gridss.wdl +++ b/gridss.wdl @@ -94,7 +94,7 @@ task GRIDSS { File? gridssProperties Int jvmHeapSizeGb = 64 - Int threads = 4 + Int threads = 8 Int timeMinutes = ceil(4320 / threads) + 10 String dockerImage = "quay.io/biocontainers/gridss:2.12.0--h270b39a_1" } @@ -163,10 +163,10 @@ task GridssAnnotateVcfRepeatmasker { File gridssVcfIndex String outputPath = "./gridss.repeatmasker_annotated.vcf.gz" - String memory = "50G" - Int threads = 4 + String memory = "25G" + Int threads = 8 String dockerImage = "quay.io/biocontainers/gridss:2.12.0--h270b39a_1" - Int timeMinutes = 2880 + Int timeMinutes = 1440 } command { diff --git a/hmftools.wdl b/hmftools.wdl index 199d7d88130a3eb8b4f9a9ad3925436296a3e142..f8b13c66a2eacfffd19323cc50712fe49986c9a8 100644 --- a/hmftools.wdl +++ b/hmftools.wdl @@ -799,10 +799,10 @@ task Sage { String? mnvFilterEnabled File? coverageBed - Int threads = 2 + Int threads = 4 String javaXmx = "50G" String memory = "60G" - Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 8 / threads) + Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 9 / threads) String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_0" } diff --git a/peach.wdl b/peach.wdl index b57842f78a23ddc552b9b32ffc37e38d62cb3d6d..af44daecfc342630d78866d93767b260147d1a0e 100644 --- a/peach.wdl +++ b/peach.wdl @@ -30,9 +30,9 @@ task Peach { String outputDir = "./peach" File panelJson - String memory = "8G" + String memory = "2G" String dockerImage = "quay.io/biowdl/peach:v1.0" - Int timeMinutes = 20 + Int timeMinutes = 5 } command {