From 4431b259d68024b057fe5cfd5dc4de2424450d4b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 24 Oct 2022 15:46:09 +0200
Subject: [PATCH] Make sure index task works
---
bwa.wdl | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index f79a219..a129ebb 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -119,7 +119,7 @@ task Index {
input {
File fasta
}
- File indexedFile = "reference.fasta"
+ String indexedFile = "reference.fasta"
command {
set -e
@@ -128,9 +128,9 @@ task Index {
}
output {
- BwaIndex index = {
- "fastaFile": indexedFile,
- "indexFiles": [
+ BwaIndex index = object {
+ fastaFile: indexedFile,
+ indexFiles: [
indexedFile + ".amb",
indexedFile + ".ann",
indexedFile + ".bwt",
@@ -139,4 +139,10 @@ task Index {
]
}
}
+
+ runtime {
+ docker: "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"
+ cpu: 1
+ memory: "~{size(fasta, 'G') + 1}GiB"
+ }
}
\ No newline at end of file
--
GitLab