From d9265c317f404c26f0bfd0a2950fd716e9204e56 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 28 Apr 2020 13:36:45 +0200
Subject: [PATCH] Fix quotations in samtools sort.
---
CHANGELOG.md | 1 +
samtools.wdl | 4 ++--
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4a95484..c12fcec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
-->
version 3.1.0
---------------------------
++ Samtools: Fix quotations in sort command.
+ Samtools SortByName is now called Sort.
+ Generalize sort task to now also sort by position, instead of just read name.
+ Add CreateSequenceDictionary task to picard.
diff --git a/samtools.wdl b/samtools.wdl
index ad7799c..5521c6a 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -191,10 +191,10 @@ task Sort {
set -e
mkdir -p "$(dirname ~{outputPath})"
samtools sort \
- "-l " ~{compressionLevel} \
+ -l ~{compressionLevel} \
~{true="-n" false="" sortByName} \
~{"--threads " + threads} \
- "-o " ~{outputPath} \
+ -o ~{outputPath} \
~{inputBam}
}
--
GitLab