From e8205127a0bdf5dcce0b74086e4b05c1db35aa4d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 4 Sep 2019 07:51:55 +0200
Subject: [PATCH] fix busybox mkdir
---
fastqsplitter.wdl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/fastqsplitter.wdl b/fastqsplitter.wdl
index 846193e..cbbb7f3 100644
--- a/fastqsplitter.wdl
+++ b/fastqsplitter.wdl
@@ -34,9 +34,12 @@ task Fastqsplitter {
Int cores = 1 + ceil(0.5 * length(outputPaths))
}
+ # Busybox mkdir does not accept multiple paths.
command <<<
set -e
- mkdir -p $(dirname ~{sep=' ' outputPaths})
+ for FILE in ~{sep=' ' outputPaths}
+ do mkdir -p $(dirname $FILE)
+ done
fastqsplitter \
~{"-c " + compressionLevel} \
~{"-t " + threadsPerFile} \
--
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