From 5a4a0440ff1bd297aa8255aeb557a9a9bdab0c7c Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 6 Mar 2018 11:14:03 +0100
Subject: [PATCH] solve poretools issue
---
poretools.wdl | 28 +++++++++++++++++-----------
1 file changed, 17 insertions(+), 11 deletions(-)
diff --git a/poretools.wdl b/poretools.wdl
index fcbaff7..95dce6c 100644
--- a/poretools.wdl
+++ b/poretools.wdl
@@ -1,5 +1,5 @@
task fastq {
- Array[String]+ files # Array[String]+ instead of Array[File]+ to allow for globs
+ Array[File]+ files # Files should exist! Also accepts multiple directories (unlike poretools).
String outputFile
String? preCommand
String? type
@@ -16,16 +16,22 @@ task fastq {
mkdir -p $(dirname ${outputFile})
${preCommand}
- poretools fastq \
- ${"--type " + type} \
- ${"--start " + start } \
- ${"--end " + end } \
- ${"--min-length " + minLength } \
- ${"--max-length " + maxLength } \
- ${true="--high-quality" false="" highQuality} \
- ${true="--normal-quality" false="" normalQuality} \
- ${"--group " + group} \
- ${sep=" " files} ${true="| gzip " false="" gzip}> ${outputFile}
+ (
+ # Allow for multiple directory input by looping over files
+ for file in ${sep=" " files}
+ do
+ poretools fastq \
+ ${"--type " + type} \
+ ${"--start " + start } \
+ ${"--end " + end } \
+ ${"--min-length " + minLength } \
+ ${"--max-length " + maxLength } \
+ ${true="--high-quality" false="" highQuality} \
+ ${true="--normal-quality" false="" normalQuality} \
+ ${"--group " + group} \
+ $file
+ done
+ ) ${true="| gzip " false="" gzip}> ${outputFile}
}
output {
--
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