From f37b2874cd9f35f9bbb014103f73a9b6a17ebf6a Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 10 Jan 2020 11:05:29 +0100
Subject: [PATCH] add parameter_meta to bowtie
---
bowtie.wdl | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/bowtie.wdl b/bowtie.wdl
index 72a3964..18fd614 100644
--- a/bowtie.wdl
+++ b/bowtie.wdl
@@ -80,6 +80,27 @@ task Bowtie {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ readsUpstream: {description: "The first-/single-end fastq files.", category: "required"}
+ readsDownstream: {description: "The second-end fastq files.", category: "common"}
+ outputPath: {description: "The location the output BAM file should be written to.", category: "common"}
+ indexFiles: {description: "The index files for bowtie.", category: "required"}
+ seedmms: {description: "Equivalent to bowtie's `--seedmms` option.", category: "advanced"}
+ seedlen: {description: "Equivalent to bowtie's `--seedlen` option.", category: "advanced"}
+ k: {description: "Equivalent to bowtie's `-k` option.", category: "advanced"}
+ best: {description: "Equivalent to bowtie's `--best` flag.", category: "advanced"}
+ strata: {description: "Equivalent to bowtie's `--strata` flag.", category: "advanced"}
+ allowContain: {description: "Equivalent to bowtie's `--allow-contain` flag.", category: "advanced"}
+ samRG: {description: "Equivalent to bowtie's `--sam-RG` option.", category: "advanced"}
+
+ picardXmx: {description: "The maximum memory available to the picard (used for sorting the output). Should be lower than `memory` to accommodate JVM overhead and bowtie's memory usage.",
+ category: "advanced"}
+ threads: {description: "The number of threads to use.", 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 choose not to address.",
+ category: "advanced"}
+ }
}
struct BowtieIndex {
--
GitLab