From 31b9347abb1e5587b273fff189f2160994238dbd Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jan 2018 16:39:16 +0100
Subject: [PATCH] some debugging
---
bioconda.wdl | 1 +
cutadapt.wdl | 2 +-
fastqc.wdl | 2 +-
3 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/bioconda.wdl b/bioconda.wdl
index f8c14e7..0600ff7 100644
--- a/bioconda.wdl
+++ b/bioconda.wdl
@@ -20,5 +20,6 @@ task installPrefix {
}
output {
File condaEnvPath=prefix
+ File condaJson=stdout()
}
}
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 7e44041..88959a7 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -97,7 +97,7 @@ task cutadapt {
${read1} ${read2}
}
output{
- File report = file(stdout())
+ File report = stdout()
File cutRead1 = read1output
File? cutRead2 = read2output
File? tooLongOutput=tooLongOutputPath
diff --git a/fastqc.wdl b/fastqc.wdl
index 65b9509..a19d45c 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -39,7 +39,7 @@ task fastqc {
}
output {
- String reportDir = outdirPath + "/" + sub(basename(seqFile),"\..*$","_fastqc")
+ String reportDir = outdirPath + "/" + sub(basename(seqFile), "..*$", "_fastqc")
File rawReport = reportDir + "/fastqc_data.txt"
File htmlReport = reportDir + "fastqc_report.html"
File summary = reportDir + "/summary.txt"
--
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