From 30bfec34b6664337bb37a6f270da0d7b8991e14b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 10:05:52 +0200
Subject: [PATCH] evaluate outputpaths before command section
---
fastqc.wdl | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index b361f10..f0fd2fe 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -15,7 +15,11 @@ task fastqc {
File? limits
Int? kmers
String? dir
-
+ # Chops of the .gz extension if present.
+ String name = sub(seqFile, "\\.gz$","")
+ # This regex chops of the extension and replaces it with _fastqc for the reportdir.
+ # Just as fastqc does it.
+ String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
command {
set -e -o pipefail
${preCommand}
@@ -40,11 +44,6 @@ task fastqc {
}
output {
- # Chops of the .gz extension if present.
- String name = sub(seqFile, "\\.gz$","")
- # This regex chops of the extension and replaces it with _fastqc for the reportdir.
- # Just as fastqc does it.
- String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
File rawReport = reportDir + "/fastqc_data.txt"
File htmlReport = reportDir + "/fastqc_report.html"
File summary = reportDir + "/summary.txt"
--
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