From 830a39b81c2c955cb9816a890bba07d58b8e41c7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 14 Jun 2018 10:32:28 +0200
Subject: [PATCH] Revert "Fixing output"

This reverts commit 17af04e
---
 fastqc.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fastqc.wdl b/fastqc.wdl
index a4cde25..635fa74 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -16,7 +16,7 @@ task fastqc {
     Int? kmers
     String? dir
     # Chops of the .gz extension if present.
-    String name = sub(sub(sub(seqFile, "\\.gz$",""), "\\.fq$",""), "\\.fastq$","")
+    String name = sub(sub(seqFile, "\\.gz$",""), "\\.fq$|\\.fastq$","")
     # This regex chops of the extension and replaces it with _fastqc for the reportdir.
     # Just as fastqc does it.
     String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
-- 
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