From 54ac9d0c41f74c578f2418bc76483d1081695369 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 19 Nov 2020 15:18:41 +0100
Subject: [PATCH] add missed argument in purple
---
hmftools.wdl | 3 +++
1 file changed, 3 insertions(+)
diff --git a/hmftools.wdl b/hmftools.wdl
index ed2914b..fc56ecd 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -283,6 +283,7 @@ task Purple {
File referenceFasta
File referenceFastaFai
File referenceFastaDict
+ File driverGenePanel
File hotspots
Int threads = 1
@@ -306,6 +307,7 @@ task Purple {
-circos /usr/local/bin/circos \
-ref_genome ~{referenceFasta} \
-driver_catalog \
+ -driver_gene_panel ~{driverGenePanel} \
-hotspots ~{hotspots} \
-threads ~{threads}
@@ -340,6 +342,7 @@ task Purple {
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ driverGenePanel: {description: "A bed file describing the driver gene panel.", category: "required"}
hotspots: {description: "A vcf file with hotspot variant sites.", category: "required"}
threads: {description: "The number of threads the program will use.", category: "advanced"}
--
GitLab