From 4860b40d611f07ea62822a4a35c4bec70d45a7dd Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Jan 2018 16:05:37 +0100
Subject: [PATCH] allow gzipped files
---
fastqc.wdl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index 630ee15..657c792 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -40,10 +40,11 @@ task fastqc {
}
output {
- # Apparently, the escape character needs to be escaped in regexes.
+ # Chops of the .gz extension if present.
+ String name = sub(seqFile, "\\.gz$","")
# This regex chops of the extension and replaces it with _fastqc for the reportdir.
# Just as fastqc does it.
- String reportDir = outdirPath + "/" + sub(basename(seqFile), "\\.[^\\.]*$", "_fastqc")
+ String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
File rawReport = reportDir + "/fastqc_data.txt"
File htmlReport = reportDir + "/fastqc_report.html"
File summary = reportDir + "/summary.txt"
--
GitLab