diff --git a/CHANGELOG.md b/CHANGELOG.md index f750b212206de4b6e44ae880ebfdf5f4d4e6f064..be0e5a7c11d5841b357a12cba2e0f96da0586188 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ that users understand how the changes affect the new version. --> version 5.1.0-dev --------------------------- ++ Purple's `somaticRainfallPlot` output is now optional and included in + the `plots` output as well. + Bedtools coverage's timeMinutes now defaults to `320`. + Gridss' runtime attribute defaults were changed to: + jvmHeapSizeGb: `64` diff --git a/hmftools.wdl b/hmftools.wdl index 1542bdfc6752cee489f6c5fed2cf8752db376456..f878181ae46dbb79477842a7c0dde3cb05bd6076 100644 --- a/hmftools.wdl +++ b/hmftools.wdl @@ -1133,7 +1133,7 @@ task Purple { File segmentPlot = "~{outputDir}/plot/~{tumorName}.segment.png" File somaticClonalityPlot = "~{outputDir}/plot/~{tumorName}.somatic.clonality.png" File somaticPlot = "~{outputDir}/plot/~{tumorName}.somatic.png" - File somaticRainfallPlot = "~{outputDir}/plot/~{tumorName}.somatic.rainfall.png" + File? somaticRainfallPlot = "~{outputDir}/plot/~{tumorName}.somatic.rainfall.png" File circosNormalRatio = "~{outputDir}/circos/~{referenceName}.ratio.circos" File circosBaf = "~{outputDir}/circos/~{tumorName}.baf.circos" File circosConf = "~{outputDir}/circos/~{tumorName}.circos.conf" @@ -1150,8 +1150,8 @@ task Purple { purpleSegmentTsv, purpleSomaticClonalityTsv, purpleSomaticHistTsv, purpleSomaticVcf, purpleSomaticVcfIndex, purpleSvVcf, purpleSvVcfIndex, purpleVersion, purpleGermlineVcf, purpleGermlineVcfIndex, driverCatalogGermlineTsv] - Array[File] plots = [circosPlot, copynumberPlot, inputPlot, mapPlot, purityRangePlot, - segmentPlot, somaticClonalityPlot, somaticPlot] + Array[File] plots = select_all([circosPlot, copynumberPlot, inputPlot, mapPlot, purityRangePlot, + segmentPlot, somaticClonalityPlot, somaticPlot, somaticRainfallPlot]) Array[File] circos = [circosNormalRatio, circosConf, circosIndel, circosLink, circosTumorRatio, circosGaps, circosBaf, circosCnv, circosInputConf, circosMap, circosSnp]