From f2f7411a7b32bda18bba6eb8ee83606fa635f9e0 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 15 Jun 2021 12:43:37 +0200
Subject: [PATCH] Add directory creation to samtools fastq.
---
CHANGELOG.md | 3 +--
samtools.wdl | 2 ++
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 11a92d8..e724269 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,8 +10,7 @@ that users understand how the changes affect the new version.
version 5.0.0-dev
---------------------------
-+ Change the way localization of the input bam files and index are handled
- in the bam2fastx tasks.
++ Samtools: Add mkdir line to `Fastq` task.
+ Add new parameters from CCS version 6.0.0 and add two new outputs:
`ccs_report.txt` & `zmw_metrics.json.gz`.
+ Change CutAdapt memory to `5G`.
diff --git a/samtools.wdl b/samtools.wdl
index 9042a0d..46d1eb7 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -122,6 +122,8 @@ task Fastq {
}
command {
+ set -e
+ mkdir -p "$(dirname ~{outputRead1})"
samtools fastq \
~{true="-1" false="-s" defined(outputRead2)} ~{outputRead1} \
~{"-2 " + outputRead2} \
--
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