From 87c555a6e15cb4eb2d034e664da9413115703db6 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Jan 2018 10:49:01 +0100
Subject: [PATCH] debugged output file
---
fastqc.wdl | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index bd660f7..8be2258 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -36,12 +36,16 @@ task fastqc {
${"--kmers " + kmers} \
${"--dir " + dir} \
${seqFile}
+
}
output {
- String reportDir = outdirPath + "/" + sub(basename(seqFile), "..*$", "_fastqc")
+ # Apparently, the escape character needs to be escaped in regexes.
+ # 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")
File rawReport = reportDir + "/fastqc_data.txt"
- File htmlReport = reportDir + "fastqc_report.html"
+ File htmlReport = reportDir + "/fastqc_report.html"
File summary = reportDir + "/summary.txt"
File adapterContent = reportDir + "/Images/adapter_content.png"
File duplicationLevels = reportDir + "/Images/duplication_levels.png"
--
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