From 996a5fefa828ca89191696d8284bff73c6e3f6cc Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 24 Feb 2020 14:46:13 +0100
Subject: [PATCH] add selectvariants tasks
---
gatk.wdl | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 56 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index 1aa23ea..754bbc6 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1347,6 +1347,62 @@ task PreprocessIntervals {
}
}
+task SelectVariants {
+ input {
+ File referenceFasta
+ File referenceFastaDict
+ File referenceFastaFai
+ File inputVcf
+ File inputVcfIndex
+ String outputPath = "output.vcf.gz"
+ String? selectTypeToInclude
+ Array[File] intervals = []
+ String memory = "16G"
+ String javaXmx = "4G"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ }
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ gatk --java-options -Xmx~{javaXmx} \
+ SelectVariants \
+ -R ~{referenceFasta} \
+ -V ~{inputVcf} \
+ ~{"--select-type-to-include " + selectTypeToInclude} \
+ ~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals}
+ }
+
+ output {
+ File outputVcf = outputPath
+ File outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: memory
+ }
+
+ parameter_meta {
+ inputVcf: {description: "The VCF input file.", category: "required"}
+ inputVcfIndex: {description: "The input VCF file's index.", category: "required"}
+ referenceFasta: {description: "The reference fasta file which was also used for mapping.",
+ category: "required"}
+ referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
+ category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ selectTypeToInclude: {description: "Select only a certain type of variants from the input file", category: "common"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "required"}
+ intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
+
+ 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.",
+ 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"}
+ }
+}
+
task SplitNCigarReads {
input {
File inputBam
--
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