From efc225af1afcf2ab4e0740d93a6c07d093e3d102 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 25 Feb 2020 09:28:58 +0100
Subject: [PATCH] update tasks
---
gatk.wdl | 3 ++-
rtg.wdl | 10 ++++++----
2 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 754bbc6..4029ae0 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1370,7 +1370,8 @@ task SelectVariants {
-R ~{referenceFasta} \
-V ~{inputVcf} \
~{"--select-type-to-include " + selectTypeToInclude} \
- ~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals}
+ ~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals} \
+ -O ~{outputPath}
}
output {
diff --git a/rtg.wdl b/rtg.wdl
index bc5aa27..278fd01 100644
--- a/rtg.wdl
+++ b/rtg.wdl
@@ -66,7 +66,6 @@ task VcfEval {
File? evaluationRegions
File? bedRegions
String outputDir = "output/"
- String? region
File template
Boolean allRecords = false
Boolean decompose = false
@@ -79,9 +78,9 @@ task VcfEval {
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
}
- command {
+ command <<<
set -e
- mkdir -p ~{outputDir}
+ mkdir -p "$(dirname ~{outputDir})"
rtg vcfeval \
--baseline ~{baseline} \
--calls ~{calls} \
@@ -96,7 +95,7 @@ task VcfEval {
~{true="--squash-ploidy" false="" squashPloidy} \
~{"--output-mode " + outputMode} \
--threads ~{threads}
- }
+ >>>
output {
File falseNegativesVcf = outputDir + "/fn.vcf.gz"
@@ -125,6 +124,9 @@ task VcfEval {
calls: {description: "VCF file containing called variants", category: "required"}
callsIndex: {description: "The call's VCF index", category: "required"}
outputDir: {description: "Directory for output", category: "advanced"}
+ bedRegions: {description: "if set, only read VCF records that overlap the ranges contained in the specified BED file", category: "advanced"}
+ evaluationRegions: {description: "if set, evaluate within regions contained in the supplied BED file, allowing transborder matches. To be used for truth-set high-confidence regions or other regions of interest where region boundary effects should be minimized",
+ category: "advanced"}
template: {description: "SDF of the reference genome the variants are called against", category: "required"}
allRecords: {description: "use all records regardless of FILTER status (Default is to only process records where FILTER is \".\" or \"PASS\")",
category: "common"}
--
GitLab