Verified Commit 81a2d4bb authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Bowtie2: modify single-end to have a file_id variable like for

paired-end
parent 52e09505
......@@ -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
"""
......
......@@ -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
"""
......
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