From fa4a67859efa5253327772fedc935cffedbfb06e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jan 2018 17:28:38 +0100
Subject: [PATCH] some debugging
---
cutadapt.wdl | 2 +-
fastqc.wdl | 17 +++++++++++------
2 files changed, 12 insertions(+), 7 deletions(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 88959a7..f2bdf49 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -111,6 +111,6 @@ task cutadapt {
File? wildcardFile=wildcardFilePath
}
runtime {
- cpu: select_first(cores)
+ cpu: select_first([cores])
}
}
\ No newline at end of file
diff --git a/fastqc.wdl b/fastqc.wdl
index a19d45c..bd660f7 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -21,7 +21,7 @@ task fastqc {
${"source activate " + condaEnv}
mkdir -p ${outdirPath}
fastqc \
- ${"--outdir " + outdirPath}
+ ${"--outdir " + outdirPath} \
${true="--casava" false="" casava} \
${true="--nano" false="" nano} \
${true="--nofilter" false="" noFilter} \
@@ -55,21 +55,24 @@ task fastqc {
}
runtime {
- cpu: select_first(threads)
+ cpu: select_first([threads])
}
}
task extractAdapters {
File extractAdaptersFastqcJar
File inputFile
- String? adapterOutputFilePath
- String? contamsOutputFilePath
+ String outputDir
+ String? adapterOutputFilePath = outputDir + "/adapter.list"
+ String? contamsOutputFilePath = outputDir + "/contaminations.list"
Boolean? skipContams
File? knownContamFile
File? knownAdapterFile
Float? adapterCutoff
Boolean? outputAsFasta
command {
+ set -e
+ mkdir -p ${outputDir}
java -jar ${extractAdaptersFastqcJar} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
@@ -82,7 +85,9 @@ task extractAdapters {
}
output {
- File? adapterOutputFile = adapterOutputFilePath
- File? contamsOutputFile = contamsOutputFilePath
+ File adapterOutputFile = select_first([adapterOutputFilePath])
+ File contamsOutputFile = select_first([contamsOutputFilePath])
+ Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
+ Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
}
}
\ No newline at end of file
--
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