From 8bed940cc18c415fd93f5108bed3f0f7414eabda Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 23 Jan 2020 16:29:24 +0100
Subject: [PATCH] update parameter meta
---
common.wdl | 6 ++++++
gatk.wdl | 4 +++-
2 files changed, 9 insertions(+), 1 deletion(-)
diff --git a/common.wdl b/common.wdl
index 92fd586..87dcce1 100644
--- a/common.wdl
+++ b/common.wdl
@@ -174,6 +174,12 @@ task TextToFile {
File out = outputFile
}
+ parameter_meta {
+ text: {description: "The text to print", category: "required"}
+ outputFile: {description: "The name of the output file", category: "common"}
+ 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"}
+ }
runtime {
memory: "1G"
docker: dockerImage
diff --git a/gatk.wdl b/gatk.wdl
index b44620a..0b4c71c 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -342,8 +342,10 @@ task HaplotypeCallerGvcf {
parameter_meta {
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
- intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"}
+ intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "common"}
+ excludeIntervalList: {description: "Bed files or interval lists describing the regions to NOT operate on.", category: "common"}
gvcfPath: {description: "The location to write the output GVCF to.", category: "required"}
+ ploidy: {description: "The ploidy with which the variants should be called.", category: "common"}
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.",
--
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