From 9e868dbcfbd4374ef6e04fbe389bf550be67a6ba Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 8 Nov 2021 14:26:37 +0100
Subject: [PATCH] add img input for virusbreakend
---
gridss.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gridss.wdl b/gridss.wdl
index 03193cc..b36d659 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -207,6 +207,7 @@ task Virusbreakend {
File bam
File bamIndex
File referenceFasta
+ File referenceImg
File virusbreakendDB
String outputPath = "./virusbreakend.vcf"
@@ -246,6 +247,7 @@ task Virusbreakend {
bam: {description: "A BAM file.", category: "required"}
bamIndex: {description: "The index for the BAM file.", category: "required"}
referenceFasta: {description: "The fasta of the reference genome.", category: "required"}
+ referenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the reference.", category: "required"}
virusbreakendDB: {description: "A .tar.gz containing the virusbreakend database.", category: "required"}
outputPath: {description: "The path the output should be written to.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
--
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