From 17af04e85d0f7b9cb40619fdde9bb6b7b4b4a50a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 14 Jun 2018 07:46:03 +0200
Subject: [PATCH] Fixing output
---
fastqc.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index 635fa74..a4cde25 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(seqFile, "\\.gz$",""), "\\.fq$|\\.fastq$","")
+ String name = sub(sub(sub(seqFile, "\\.gz$",""), "\\.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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