From 24cc6213026dbe1de017ebeabc2de7fbfad912ae Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 8 Aug 2022 11:11:48 +0200
Subject: [PATCH] make purple's somaticRainfallPlot output optional
---
CHANGELOG.md | 2 ++
hmftools.wdl | 6 +++---
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f750b21..be0e5a7 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 1542bdf..f878181 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]
--
GitLab