From 1de16f9a9e3a94768418d32a407759d131f968dc Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 15 Apr 2021 11:24:04 +0200
Subject: [PATCH] bwa: handle dict as file_id for mapping_fastq
---
src/nf_modules/bwa/main.nf | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index a1c8fa0d..dd5cc390 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -47,14 +47,11 @@ process mapping_fastq {
script:
if (file_id instanceof List){
+ library = file_id[0]
file_prefix = file_id[0]
- if (file_id.containsKey('library')) {
- library = file_id.library
- file_prefix = file_id.id
- } else {
- library = file_id[0]
- file_prefix = file_id[0]
- }
+ else if (file_id.containsKey('library')) {
+ library = file_id.library
+ file_prefix = file_id.id
} else {
library = file_id
file_prefix = file_id
--
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