From 80d9b71d1563af304eea0110df6e2a32a16d816d Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Mon, 20 Aug 2018 18:13:15 +0200
Subject: [PATCH] Added sctruct for index files
---
bwa.wdl | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 01d1b7d..ba0023a 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -5,8 +5,7 @@ task Mem {
String? preCommand
File inputR1
File? inputR2
- File referenceFasta
- Array[File] indexFiles # These indexFiles need to be added, otherwise cromwell will not find them.
+ BwaIndex bwaIndex
String outputPath
String? readgroup
@@ -20,7 +19,7 @@ task Mem {
~{preCommand}
bwa mem ~{"-t " + threads} \
~{"-R '" + readgroup + "'"} \
- ~{referenceFasta} \
+ ~{bwaIndex.fastaFile} \
~{inputR1} \
~{inputR2} \
| samtools sort --output-fmt BAM - > ~{outputPath}
@@ -75,3 +74,7 @@ task Index {
}
}
+struct BwaIndex {
+ File fastaFile
+ Array[File] indexFiles
+}
--
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