From ca368e7e5a4ff8c1d4776d0095c0d62aeb5b1083 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 6 Jul 2020 13:41:56 +0200
Subject: [PATCH] add parameter_meta
---
bwa.wdl | 1 +
picard.wdl | 3 ++-
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index 4a0e86a..78881ad 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -78,6 +78,7 @@ task Mem {
memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
+ compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
diff --git a/picard.wdl b/picard.wdl
index 0e877f2..c090455 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -402,7 +402,8 @@ task GatherBamFiles {
inputBams: {description: "The BAM files to be merged together.", category: "required"}
inputBamsIndex: {description: "The indexes of the input BAM files.", category: "required"}
outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "required"}
-
+ compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
+ createMd5File: {decription: "Whether to create an md5 file of the output BAM.", category: "advanced"}
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.",
category: "advanced"}
--
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