From 81a2d4bb7984248a13736ac9aa74cf452b0d5b95 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 2 Aug 2018 16:51:11 +0200
Subject: [PATCH] Bowtie2: modify single-end to have a file_id variable like
for paired-end
---
src/nf_modules/Bowtie2/bowtie2.nf | 13 +++++++------
src/nf_modules/Bowtie2/tests/mapping_single.nf | 13 +++++++------
2 files changed, 14 insertions(+), 12 deletions(-)
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index d35c344..efee164 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -101,6 +101,7 @@ log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -108,16 +109,16 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
file index from index_files.collect()
output:
- file "*.bam" into bam_files
+ set file_id, "*.bam" into bam_files
file "*_report.txt" into mapping_report
script:
@@ -130,10 +131,10 @@ process mapping_fastq {
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-U ${reads} 2> \
-${reads.baseName}_bowtie2_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
+${file_id}_bowtie2_report.txt | \
+samtools view -Sb - > ${file_id}.bam
-if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${file_id}_bowtie2_report.txt; then
exit 1
fi
"""
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index 5f6a9de..6667699 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -6,6 +6,7 @@ log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
Channel
.fromPath( params.index )
@@ -13,16 +14,16 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$reads.baseName"
+ tag "$file_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
- file reads from fastq_files
+ set file_id, file(reads) from fastq_files
file index from index_files.collect()
output:
- file "*.bam" into bam_files
+ set file_id, "*.bam" into bam_files
file "*_report.txt" into mapping_report
script:
@@ -35,10 +36,10 @@ process mapping_fastq {
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-U ${reads} 2> \
-${reads.baseName}_bowtie2_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
+${file_id}_bowtie2_report.txt | \
+samtools view -Sb - > ${file_id}.bam
-if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${file_id}_bowtie2_report.txt; then
exit 1
fi
"""
--
GitLab