From f05d968d69d6c3a41b03a761a4a4838e5889df6c Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 24 Oct 2022 14:45:15 +0200
Subject: [PATCH] Add a Bwa index task
---
bwa.wdl | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/bwa.wdl b/bwa.wdl
index d4f4495..f79a219 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -114,3 +114,29 @@ struct BwaIndex {
File fastaFile
Array[File] indexFiles
}
+
+task Index {
+ input {
+ File fasta
+ }
+ File indexedFile = "reference.fasta"
+
+ command {
+ set -e
+ cp ~{fasta} ~{indexedFile}
+ bwa index ~{indexedFile}
+ }
+
+ output {
+ BwaIndex index = {
+ "fastaFile": indexedFile,
+ "indexFiles": [
+ indexedFile + ".amb",
+ indexedFile + ".ann",
+ indexedFile + ".bwt",
+ indexedFile + ".pac",
+ indexedFile + ".sa"
+ ]
+ }
+ }
+}
\ No newline at end of file
--
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