From 2467174555e85c5b4cf819018afd44a8b5f24af8 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 25 Feb 2022 14:19:08 +0100
Subject: [PATCH] update virus-interpreter to 1.2
---
hmftools.wdl | 22 ++++++++++++++--------
1 file changed, 14 insertions(+), 8 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index 7f73931..65187f4 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -1099,25 +1099,29 @@ task Sage {
task VirusInterpreter {
input {
String sampleId
+ File purplePurityTsv
+ File prupleQcFile
+ File tumorSampleWgsMetricsFile
File virusBreakendTsv
File taxonomyDbTsv
- File virusInterpretationTsv
- File virusBlacklistTsv
+ File virusReportingDbTsv
String outputDir = "."
String memory = "3G"
String javaXmx = "2G"
Int timeMinutes = 15
- String dockerImage = "quay.io/biowdl/virus-interpreter:1.0"
+ String dockerImage = "quay.io/biowdl/virus-interpreter:1.2"
}
command {
- virus-interpreter -Xmx~{javaXmx} \
+ virus-interpreter -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-sample_id ~{sampleId} \
+ -purple_purity_tsv ~{purplePurityTsv} \
+ -purple_qc_file ~{prupleQcFile} \
+ -tumor_sample_wgs_metrics_file ~{tumorSampleWgsMetricsFile} \
-virus_breakend_tsv ~{virusBreakendTsv} \
-taxonomy_db_tsv ~{taxonomyDbTsv} \
- -virus_interpretation_tsv ~{virusInterpretationTsv} \
- -virus_blacklist_tsv ~{virusBlacklistTsv} \
+ -virus_reporting_db_tsv ~{virusReportingDbTsv} \
-output_dir ~{outputDir}
}
@@ -1133,10 +1137,12 @@ task VirusInterpreter {
parameter_meta {
sampleId: {description: "The name of the sample.", category: "required"}
+ purplePurityTsv: {description: "The purity file produced by purple.", category: "required"}
+ prupleQcFile: {description: "The QC file produced by purple.", category: "required"}
+ tumorSampleWgsMetricsFile: {description: "The picard WGS metrics file for this sample.", category: "required"}
virusBreakendTsv: {description: "The TSV output from virusbreakend.", category: "required"}
taxonomyDbTsv: {description: "A taxonomy database tsv.", category: "required"}
- virusInterpretationTsv: {description: "A virus interpretation tsv.", category: "required"}
- virusBlacklistTsv: {description: "A virus blacklist tsv.", category: "required"}
+ virusReportingDbTsv: {description: "A virus reporting tsv.", category: "required"}
outputDir: {description: "The directory the output will be written to.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
--
GitLab