From 138d36067afd359310c5a65d77c873527a013225 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 14 Jun 2018 07:25:06 +0200
Subject: [PATCH] Added glob's to output files
---
fastqc.wdl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/fastqc.wdl b/fastqc.wdl
index d9135f7..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(seqFile, "\\.gz$","")
+ String name = sub(sub(seqFile, "\\.gz$",""), "\\.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")
@@ -44,9 +44,9 @@ task fastqc {
}
output {
- File rawReport = reportDir + "/fastqc_data.txt"
- File htmlReport = reportDir + "/fastqc_report.html"
- File summary = reportDir + "/summary.txt"
+ File rawReport = select_first(glob(outdirPath + "/" + name + "*_fastqc/fastqc_data.txt"))
+ File htmlReport = select_first(glob(outdirPath + "/" + name + "*_fastqc/fastqc_report.html"))
+ File summary = select_first(glob(outdirPath + "/" + name + "*_fastqc/summary.txt"))
Array[File] images = glob(reportDir + "/Images/*.png")
}
--
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