From 71eb31625ea9803f4d7c2223e2f4dd8be9cc11bf Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 14:43:25 +0100
Subject: [PATCH] bwa: fix file_id definition
---
src/nf_modules/bwa/main.nf | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 7d2abd12..0331dd9e 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -37,16 +37,18 @@ process mapping_fastq {
script:
if (file_id.containsKey('library')) {
library = file_id.library
+ id = file_id.id
} else {
library = file_id
+ id = file_id
}
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
"""
bwa mem -t ${task.cpus} \
-R '${bwa_mem_R}' \
${index_id} ${reads[0]} ${reads[1]} 2> \
- ${file_id}_bwa_report.txt | \
- samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam
+ ${id}_bwa_report.txt | \
+ samtools view -@ ${task.cpus} -Sb - > ${id}.bam
"""
}
--
GitLab