From a6c3487834da5ce6b6a40ce2e966e9d899abb240 Mon Sep 17 00:00:00 2001
From: Redmar <redmar@ubuntu.com>
Date: Mon, 24 Aug 2020 09:41:30 +0200
Subject: [PATCH] Add option to ignore masked reference
---
vt.wdl | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/vt.wdl b/vt.wdl
index d4c134b..8a9f9de 100644
--- a/vt.wdl
+++ b/vt.wdl
@@ -26,6 +26,7 @@ task Normalize {
File inputVCFIndex
File referenceFasta
File referenceFastaFai
+ Boolean ignoreMaskedRef = false
String outputPath = "./vt/normalized_decomposed.vcf"
String dockerImage = "quay.io/biocontainers/vt:0.57721--hdf88d34_2"
String memory = "4G"
@@ -33,9 +34,12 @@ task Normalize {
}
command {
- set -e
+ set -eo pipefail
mkdir -p "$(dirname ~{outputPath})"
- vt normalize ~{inputVCF} -r ~{referenceFasta} | vt decompose -s - -o ~{outputPath}
+ vt normalize ~{inputVCF} \
+ -r ~{referenceFasta} \
+ ~{true="-m " false="" ignoreMaskedRef} \
+ | vt decompose -s - -o ~{outputPath}
}
output {
@@ -55,6 +59,7 @@ task Normalize {
outputPath: {description: "The location the output VCF file should be written.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ ignoreMaskedRef: {description: "Warns but does not exit when REF is inconsistent with masked reference sequence for non SNPs", category: "advanced"
memory: {description: "The memory required to run the programs", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
--
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