From d8848dc95d73402eb92483456a35eaac9040a83e Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 7 Oct 2020 14:10:05 +0200
Subject: [PATCH] Make intervals optional for gatk GenotypeGVCFs
---
gatk.wdl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index e0209a0..12416dd 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -820,7 +820,7 @@ task GenotypeGVCFs {
input {
File gvcfFile
File gvcfFileIndex
- Array[File]+ intervals
+ Array[File]? intervals
String outputPath
File referenceFasta
File referenceFastaDict
@@ -846,9 +846,9 @@ task GenotypeGVCFs {
~{"-D " + dbsnpVCF} \
~{"--pedigree " + pedigree} \
~{true="-G" false="" length(annotationGroups) > 0} ~{sep=" -G " annotationGroups} \
- --only-output-calls-starting-in-intervals \
-V ~{gvcfFile} \
- -L ~{sep=' -L ' intervals}
+ ~{true="--only-output-calls-starting-in-intervals" false="" defined(intervals)} \
+ ~{true="-L" false="" defined(intervals)} ~{sep=' -L ' intervals}
}
output {
@@ -866,7 +866,7 @@ task GenotypeGVCFs {
parameter_meta {
gvcfFile: {description: "The GVCF file to be genotyped.", category: "required"}
gvcfFileIndex: {description: "The index of the input GVCF file.", category: "required"}
- intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "optional"}
outputPath: {description: "The location to write the output VCF file to.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
--
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