From 5a740c18f7504e54a4e7dddb71e2a5f662fa9757 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 29 May 2018 10:53:35 +0200
Subject: [PATCH] make extractadaptersfastqc conda aware
---
biopet.wdl | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 8d91955..d66f97c 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -65,8 +65,8 @@ task BaseCounter {
}
}
-task extractAdapters {
- File extractAdaptersFastqcJar
+task extractAdaptersFastqc {
+ File? toolJar
File inputFile
String outputDir
String? adapterOutputFilePath = outputDir + "/adapter.list"
@@ -79,12 +79,16 @@ task extractAdapters {
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + mem + "G -jar " +toolJar
+ else "biopet-extractadaptersfastqc -Xmx" + mem + "G"
+
command {
set -e
mkdir -p ${outputDir}
- java -Xmx${mem}G -jar ${extractAdaptersFastqcJar} \
+ ${toolCommand} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
${"--contamsOutputFile " + contamsOutputFilePath } \
--
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