From b5d6e71a72124dc53eb9344ad0d6a1857bdaea69 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 7 Jul 2020 12:47:13 +0200
Subject: [PATCH] Add outputBAMcompression to STAR
---
CHANGELOG.md | 2 ++
star.wdl | 3 +++
2 files changed, 5 insertions(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index edfffb5..e70b06a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 4.0.0-develop
---------------------------
++ Alignment tasks (STAR, Hisat2, BWA) now produce BAM files at level 1
+ compression.
+ Hisat2 task has added controls for samtools.
+ Alignment tasks no longer produce BAM indexes as these are not needed
by the markduplicates step.
diff --git a/star.wdl b/star.wdl
index 4da67f7..3d0e2eb 100644
--- a/star.wdl
+++ b/star.wdl
@@ -103,6 +103,7 @@ task Star {
String? twopassMode = "Basic"
Array[String]? outSAMattrRGline
String? outSAMunmapped = "Within KeepPairs"
+ Int outBAMcompression = 1
Int? limitBAMsortRAM
Int runThreadN = 4
@@ -129,6 +130,7 @@ task Star {
--outFileNamePrefix ~{outFileNamePrefix} \
--genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \
--outSAMtype ~{outSAMtype} \
+ --outBAMcompression ~{outBAMcompression} \
--readFilesCommand ~{readFilesCommand} \
~{"--outFilterScoreMin " + outFilterScoreMin} \
~{"--outFilterScoreMinOverLread " + outFilterScoreMinOverLread} \
@@ -172,6 +174,7 @@ task Star {
limitBAMsortRAM: {description: "Equivalent to star's `--limitBAMsortRAM` option.", category: "advanced"}
runThreadN: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ outBAMcompression: {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"}
}
--
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