mapping_paired.nf

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()

  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
"""
}