From 9ddfbe5b86880cea1b650a4af6df93def494a5c3 Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Thu, 28 Jun 2018 13:28:00 +0200
Subject: [PATCH] Added mkdir step

---
 samtools.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/samtools.wdl b/samtools.wdl
index ccd99cb..b574ec5 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -54,6 +54,7 @@ task Flagstat {
     command {
         set -e -o pipefail
         ${preCommand}
+        mkdir -p $(dirname ${outputPath})
         samtools flagstat ${inputBam} > ${outputPath}
     }
 
-- 
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