diff --git a/CHANGELOG.md b/CHANGELOG.md index afd115c80dca950e7210bb8131331f8c1c3f0aa4..f750b212206de4b6e44ae880ebfdf5f4d4e6f064 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,22 @@ that users understand how the changes affect the new version. --> version 5.1.0-dev --------------------------- ++ Bedtools coverage's timeMinutes now defaults to `320`. ++ Gridss' runtime attribute defaults were changed to: + + jvmHeapSizeGb: `64` + + nonJvmMemoryGb: `10` + + threads: `12` ++ Virusbreakend's runtime attribute defaults were changed to: + + threads: `12` + + timeMinutes: `320` ++ Cobalt's timeMinutes now defaults to `480`. ++ Orange's timeMinutes now defaults to 10. ++ Sage's runtime attributes were changed to: + + threads: `32` + + javaXmx: `"16G"` + + memory: `"20G"` + + timeMinutes: `720` ++ Sambamba's runtimeMinutes nor defaults to `320`. + Added a task for CupGenerateReport. + Updated Cuppa to version 1.6. + Added a task for Gripss. diff --git a/bedtools.wdl b/bedtools.wdl index 1d956cab25c793161adee4ff00999690a42178db..80a281d65e7b560206078f11f0036aae6a90fa9f 100644 --- a/bedtools.wdl +++ b/bedtools.wdl @@ -76,7 +76,7 @@ task Coverage { String outputPath = "./coverage.tsv" String memory = "8G" - Int timeMinutes = 120 + Int timeMinutes = 320 String dockerImage = "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2" } diff --git a/gridss.wdl b/gridss.wdl index 35e41d21d6cc067384c5f73e99544ffb982d1574..add3c08f6d1c95e0febc962e48962b91329e3fe9 100644 --- a/gridss.wdl +++ b/gridss.wdl @@ -161,9 +161,9 @@ task GRIDSS { File? blacklistBed File? gridssProperties - Int jvmHeapSizeGb = 300 - Int nonJvmMemoryGb = 50 - Int threads = 4 + Int jvmHeapSizeGb = 64 + Int nonJvmMemoryGb = 10 + Int threads = 12 Int timeMinutes = ceil(7200 / threads) + 1800 String dockerImage = "quay.io/biowdl/gridss:2.12.2" } @@ -290,9 +290,9 @@ task Virusbreakend { String outputPath = "./virusbreakend.vcf" String memory = "75G" - Int threads = 8 + Int threads = 12 String dockerImage = "quay.io/biowdl/gridss:2.12.2" - Int timeMinutes = 180 + Int timeMinutes = 320 } command { diff --git a/hmftools.wdl b/hmftools.wdl index 628e2f9b00bc2f795d033c80bf5a9f73a4697600..1542bdfc6752cee489f6c5fed2cf8752db376456 100644 --- a/hmftools.wdl +++ b/hmftools.wdl @@ -114,7 +114,7 @@ task Cobalt { Int threads = 1 String memory = "5G" String javaXmx = "4G" - Int timeMinutes = 240 + Int timeMinutes = 480 String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.11--0" } @@ -780,7 +780,7 @@ task Orange { String memory = "17G" String javaXmx = "16G" - Int timeMinutes = 1440 #FIXME + Int timeMinutes = 10 String dockerImage = "quay.io/biowdl/orange:v1.6" } @@ -1225,10 +1225,10 @@ task Sage { String? mnvFilterEnabled File? coverageBed - Int threads = 4 - String javaXmx = "50G" - String memory = "51G" - Int timeMinutes = 1 + ceil(size(select_all([tumorBam, referenceBam]), "G") * 9 / threads) + Int threads = 32 + String javaXmx = "16G" + String memory = "20G" + Int timeMinutes = 720 String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_1" } diff --git a/sambamba.wdl b/sambamba.wdl index 4c2115e07dd95b2d126488a36846338b745b48fd..6696668a70f8162a4735c6f019f784d102a0c17d 100644 --- a/sambamba.wdl +++ b/sambamba.wdl @@ -28,7 +28,7 @@ task Flagstat { Int threads = 2 String memory = "8G" - Int timeMinutes = 120 + Int timeMinutes = 320 String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2" }