From c6dce99207b4059183d4649ab2acdfa4a5d66a90 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 18:50:57 +0200
Subject: [PATCH] bwa: update to match CONTRIBUTING.md
---
src/nf_modules/bwa/main.nf | 44 ++++++++++++++++++++++++--------------
1 file changed, 28 insertions(+), 16 deletions(-)
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 184192c1..047d2a51 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -1,13 +1,16 @@
version = "0.7.17"
container_url = "lbmc/bwa:${version}"
-params.index_fasta = ""
-params.mapping_fastq = ""
+params.index_fasta = ""
+params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
+ if (params.index_fasta_out != "") {
+ publishDir "results/${params.index_fasta_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(fasta)
@@ -24,10 +27,15 @@ bwa index ${params.index_fastq} -p ${fasta.simpleName} ${fasta} \
}
+params.mapping_fastq = ""
+params.mapping_fastq_out = ""
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(reads)
@@ -38,32 +46,36 @@ process mapping_fastq {
tuple val(file_id), path("${id}_bwa_report.txt"), emit: report
script:
-if (file_id.containsKey('library')) {
- library = file_id.library
- id = file_id.id
-} else {
- library = file_id
- id = file_id
-}
+ if (file_id instanceof List){
+ file_prefix = file_id[0]
+ if (file_id.containsKey('library')) {
+ library = file_id.library
+ file_prefix = file_id.id
+ } else {
+ library = file_id
+ file_prefix = file_id
+ }
+ } else {
+ file_prefix = file_id
+ }
bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina"
-if (reads instanceof List)
+ if (reads.size() == 2)
"""
bwa mem -t ${task.cpus} \
${params.mapping_fastq} \
-R '${bwa_mem_R}' \
${index_id} ${reads[0]} ${reads[1]} 2> \
- ${id}_bwa_report.txt | \
- samtools view -@ ${task.cpus} -Sb - > ${id}.bam
+ ${file_prefix}_bwa_report.txt | \
+ samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
"""
-else
-
+ else if (reads.size() == 1)
"""
bwa mem -t ${task.cpus} \
${params.mapping_fastq} \
-R '${bwa_mem_R}' \
${index_id} ${reads} 2> \
- ${id}_bwa_report.txt | \
- samtools view -@ ${task.cpus} -Sb - > ${id}.bam
+ ${file_prefix}_bwa_report.txt | \
+ samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
"""
}
--
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