From 5fdf6d20d06189bd25f8daaa5635b9c2afa3ab57 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 7 Jun 2018 11:52:55 +0200
Subject: [PATCH] fix glob issue
---
biopet.wdl | 25 ++++++++++++-------------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index cc3a915..8dd6e78 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -70,26 +70,25 @@ task BaseCounter {
task FastqSplitter {
String? preCommand
File inputFastq
- String outputPath
- Int numberChunks
- String tool_jar
- Array[Int] chunks = range(numberChunks)
+ Array[String] outputPaths
+ String toolJar
command {
set -e -o pipefail
${preCommand}
- mkdir -p ${sep=' ' prefix(outputPath + "/chunk_", chunks)}
- if [ ${numberChunks} -gt 1 ]; then
- SEP="/${basename(inputFastq)} -o "
- java -jar ${tool_jar} -I ${inputFastq} -o ${sep='$SEP' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
- else
- ln -sf ${inputFastq} ${outputPath}/chunk_0/${basename(inputFastq)}
- fi
+ for
+ mkdir -p $(dirname ${sep=') $(dirname ' outputPaths})
+ if [ ${length(outputPaths)} -gt 1 ]; then
+ java -jar ${toolJar} \
+ -I ${inputFastq} \
+ -o ${sep=' -o ' outputPaths}
+ else
+ ln -sf ${inputFastq} ${outputPaths[0]}
+ fi
}
output {
- Array[File] chunkDirs = prefix(outputPath + "/chunk_", chunks)
- String filename = basename(inputFastq)
+ Array[File] chunks = outputPaths
}
}
--
GitLab