From ece57ce10c35eb56fc5ae32b077e5ceae270e0be Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 8 Apr 2021 17:44:28 +0200
Subject: [PATCH] bwa: add params.bwa
---
src/nf_modules/bwa/main.nf | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index c6551dce..184192c1 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -1,6 +1,9 @@
version = "0.7.17"
container_url = "lbmc/bwa:${version}"
+params.index_fasta = ""
+params.mapping_fastq = ""
+
process index_fasta {
container = "${container_url}"
label "big_mem_mono_cpus"
@@ -15,7 +18,7 @@ process index_fasta {
script:
"""
-bwa index -p ${fasta.simpleName} ${fasta} \
+bwa index ${params.index_fastq} -p ${fasta.simpleName} ${fasta} \
&> ${fasta.simpleName}_bwa_report.txt
"""
}
@@ -46,6 +49,7 @@ bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumi
if (reads instanceof List)
"""
bwa mem -t ${task.cpus} \
+${params.mapping_fastq} \
-R '${bwa_mem_R}' \
${index_id} ${reads[0]} ${reads[1]} 2> \
${id}_bwa_report.txt | \
@@ -55,6 +59,7 @@ else
"""
bwa mem -t ${task.cpus} \
+${params.mapping_fastq} \
-R '${bwa_mem_R}' \
${index_id} ${reads} 2> \
${id}_bwa_report.txt | \
--
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