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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
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \