From c675c91fbc91f932c6f5018986d025993611f8a3 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 24 Feb 2022 15:14:35 +0100
Subject: [PATCH] fix linx output and health-checker command
---
hmftools.wdl | 24 ++++++++++++++++--------
1 file changed, 16 insertions(+), 8 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index 2015c12..3ab203f 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -484,8 +484,14 @@ task HealthChecker {
-tum_wgs_metrics_file ~{tumorMetrics} \
-purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
-output_dir ~{outputDir}
- test -e '~{outputDir}/~{tumorName}.HealthCheckSucceeded' && echo 'true' > '~{outputDir}/succeeded'
- test -e '~{outputDir}/~{tumorName}.HealthCheckFailed' && echo 'false' > '~{outputDir}/succeeded'
+ if [ -e '~{outputDir}/~{tumorName}.HealthCheckSucceeded' ]
+ then
+ echo 'true' > '~{outputDir}/succeeded'
+ fi
+ if [ -e '~{outputDir}/~{tumorName}.HealthCheckFailed' ]
+ then
+ echo 'false' > '~{outputDir}/succeeded'
+ fi
}
output {
@@ -531,6 +537,7 @@ task Linx {
File lineElementCsv
File knownFusionCsv
File driverGenePanel
+ Boolean writeAllVisFusions = false
#The following should be in the same directory.
File geneDataCsv
File proteinFeaturesCsv
@@ -540,7 +547,7 @@ task Linx {
String memory = "9G"
String javaXmx = "8G"
Int timeMinutes = 10
- String dockerImage = "quay.io/biocontainers/hmftools-linx:1.17--hdfd78af_0"
+ String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
}
command {
@@ -558,7 +565,8 @@ task Linx {
-check_drivers \
-driver_gene_panel ~{driverGenePanel} \
-chaining_sv_limit 0 \
- -write_vis_data
+ -write_vis_data \
+ ~{if writeAllVisFusions then "-write_all_vis_fusions" else ""}
}
output {
@@ -569,7 +577,6 @@ task Linx {
File linxFusion = "~{outputDir}/~{sampleName}.linx.fusion.tsv"
File linxLinks = "~{outputDir}/~{sampleName}.linx.links.tsv"
File linxSvs = "~{outputDir}/~{sampleName}.linx.svs.tsv"
- File linxViralInserts = "~{outputDir}/~{sampleName}.linx.viral_inserts.tsv"
File linxVisCopyNumber = "~{outputDir}/~{sampleName}.linx.vis_copy_number.tsv"
File linxVisFusion = "~{outputDir}/~{sampleName}.linx.vis_fusion.tsv"
File linxVisGeneExon = "~{outputDir}/~{sampleName}.linx.vis_gene_exon.tsv"
@@ -578,9 +585,9 @@ task Linx {
File linxVisSvData = "~{outputDir}/~{sampleName}.linx.vis_sv_data.tsv"
File linxVersion = "~{outputDir}/linx.version"
Array[File] outputs = [driverCatalog, linxBreakend, linxClusters, linxDrivers, linxFusion,
- linxLinks, linxSvs, linxViralInserts, linxVisCopyNumber,
- linxVisFusion, linxVisGeneExon, linxVisProteinDomain,
- linxVisSegments, linxVisSvData, linxVersion]
+ linxLinks, linxSvs, linxVisCopyNumber, linxVisFusion,
+ linxVisGeneExon, linxVisProteinDomain, linxVisSegments, linxVisSvData,
+ linxVersion]
}
runtime {
@@ -600,6 +607,7 @@ task Linx {
lineElementCsv: {description: "A list of known LINE source regions.", category: "required"}
knownFusionCsv: {description: "A CSV file describing known fusions.", category: "required"}
driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
+ writeAllVisFusions: {description: "Equivalent to the -write_all_vis_fusions flag.", category: "advanced"}
geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
proteinFeaturesCsv: {description: "A CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
transExonDataCsv: {description: "A CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
--
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