From 71b8929e84584cd958029a69abd71c379aa7d84f Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 25 Sep 2019 16:59:13 +0200
Subject: [PATCH] add parameter_meta for bwakit
---
bwa.wdl | 46 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/bwa.wdl b/bwa.wdl
index e4f1e12..b1079cf 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -89,6 +89,52 @@ task Kit {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ read1: {
+ description: "The first-end fastq file.",
+ category: "required"
+ }
+ read2: {
+ description: "The second-end fastq file.",
+ category: "common"
+ }
+ bwaIndex: {
+ description: "The BWA index, including a .alt file.",
+ category: "required"
+ }
+ outputPrefix: {
+ description: "The prefix of the output files, including any parent directories",
+ category: "required"
+ }
+ readgroup: {
+ description: "A readgroup identifier.",
+ category: "common"
+ }
+ sixtyFour: {
+ description: "Whether or not the index uses the '.64' suffixes.",
+ category: "common"
+ }
+ threads: {
+ description: "The number of threads to use for alignment.",
+ category: "advanced"
+ }
+ sortThreads: {
+ description: "The number of threads to use for sorting.",
+ category: "advanced"
+ }
+ memory: {
+ description: "The amount of memory this job will use.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ category: "advanced"
+ }
+
+ outputBam: "The produced BAM file."
+ outputBamIndex: "The index of the produced BAM file."
+ }
}
struct BwaIndex {
--
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