From 5f7c9945e3e06f94f7dbad39c2fe053d46e2f404 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 8 Feb 2018 16:25:16 +0100
Subject: [PATCH] solved index problem
---
bwa.wdl | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index a0f228e..4d9aad1 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -1,6 +1,7 @@
task mem {
File read1
- File referenceFile
+ File indexBase
+ Array[File] indexFiles # Not used by the command, but needed so cromwell does provide the proper links.
File? read2
String? outputFile = "aligned.bam"
String? preCommand
@@ -39,6 +40,9 @@ task mem {
Boolean? Y
Boolean? M
String? I
+ parameter_meta {
+ referenceFiles: "Should contain all the index files from the index task"
+ }
command {
set -e -o pipefail
${"mkdir -p $(dirname " + outputFile + ")"}
@@ -79,7 +83,7 @@ task mem {
${true="-Y" false="" Y } \
${true="-M" false="" M } \
${"-I " + I } \
- ${referenceFile} ${read1} ${read2} \
+ ${indexBase} ${read1} ${read2} \
| picard SortSam CREATE_INDEX=TRUE TMP_DIR=null \
INPUT=/dev/stdin SORT_ORDER=coordinate OUTPUT=${outputFile}
}
@@ -112,7 +116,9 @@ task index {
}
output {
- File indexedFasta = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
+ File indexBase = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
+ File indexedFasta = indexBase
+ Array[File] indexFiles = [indexBase + ".bwt",indexBase + ".pac",indexBase + ".sa",indexBase + ".amb",indexBase + ".ann"]
}
parameter_meta {
fasta: "Fasta file to be indexed"
--
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