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/*
* Bowtie2 :
* Imputs : fastq files
* Imputs : fasta files
* Output : bam files
*/
/* fasta indexing */
params.fasta = "$baseDir/data/bam/*.fasta"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
.set { fasta_file }
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_file
output:
file "*.index*" into index_files
script:
"""
bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
}
/*
* for paired-end data
*/
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$pair_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
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output:
file "*.bam" into bam_files
script:
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
exit 1
fi
"""
}
/*
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$reads.baseName"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*.bam" into bam_files
script:
"""
bowtie2 --very_sensitive -p ${task.cpus} -x ${index[0].baseName} \
-U ${reads} 2> \
${reads.baseName}_bowtie2_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
}