From d0b4f082c0cc876530f770a35e13fef25436cdac Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 16:11:50 +0100
Subject: [PATCH] bwa: add single_end mapping
---
src/nf_modules/bwa/main.nf | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 0331dd9e..c6551dce 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -32,7 +32,7 @@ process mapping_fastq {
output:
tuple val(file_id), path("*.bam"), emit: bam
- tuple val(file_id), path("${file_id}_bwa_report.txt"), emit: report
+ tuple val(file_id), path("${id}_bwa_report.txt"), emit: report
script:
if (file_id.containsKey('library')) {
@@ -43,6 +43,7 @@ if (file_id.containsKey('library')) {
id = file_id
}
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
+if (reads instanceof List)
"""
bwa mem -t ${task.cpus} \
-R '${bwa_mem_R}' \
@@ -50,5 +51,14 @@ ${index_id} ${reads[0]} ${reads[1]} 2> \
${id}_bwa_report.txt | \
samtools view -@ ${task.cpus} -Sb - > ${id}.bam
"""
+else
+
+"""
+bwa mem -t ${task.cpus} \
+-R '${bwa_mem_R}' \
+${index_id} ${reads} 2> \
+ ${id}_bwa_report.txt | \
+ samtools view -@ ${task.cpus} -Sb - > ${id}.bam
+"""
}
--
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