From ffe31f1fc512cec5b77c2a3a10179562480537d1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 14 Jun 2018 14:16:55 +0200
Subject: [PATCH] toolJar is a file not a string
---
biopet.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 28cd210..7a16368 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -3,7 +3,7 @@
task BaseCounter {
String? preCommand
- String? toolJar
+ File? toolJar
File bam
File bamIndex
File refFlat
@@ -72,7 +72,7 @@ task BaseCounter {
}
task ExtractAdaptersFastqc {
- String? toolJar
+ File? toolJar
File inputFile
String outputDir
String? adapterOutputFilePath = outputDir + "/adapter.list"
@@ -122,7 +122,7 @@ task FastqSplitter {
String? preCommand
File inputFastq
Array[String] outputPaths
- String? toolJar
+ File? toolJar
Float? memory
Float? memoryMultiplier
@@ -162,7 +162,7 @@ task FastqSync {
File in2
String out1path
String out2path
- String? toolJar
+ File? toolJar
Float? memory
Float? memoryMultiplier
@@ -196,7 +196,7 @@ task FastqSync {
}
task SampleConfig {
- String? toolJar
+ File? toolJar
String? preCommand
Array[File]+ inputFiles
String keyFilePath
@@ -244,7 +244,7 @@ task ScatterRegions {
File refFasta
File refDict
String outputDirPath
- String? toolJar
+ File? toolJar
Int? scatterSize
File? regions
--
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