nextflow script to merge 4 fastq lanes for Illumina data

merge_lanes.nf

params.reads = "/beegfs/sars-cov2/Test_060420"

ch_reads = Channel.fromFilePairs(params.reads + "/" + "*_R{1,2}_001.fastq.gz", flat: true)

ch_reads
        .map {
            it -> [it[0].replaceAll(~/\_L00[1,2,3,4]/,""), it[1], it[2]]
        }
        .groupTuple(by:0)
        .into {ch_reads_in; ch_test}

ch_test.countBy().subscribe{println it}

process fastq_merge_lanes {
  publishDir "$baseDir/merged_fastq", mode: "move"

  input:
  tuple sample_id, file(forward), file(reverse) from ch_reads_in
  output:
  tuple sample_id, file("${sample_id}_R1.fastq.gz"), file("${sample_id}_R2.fastq.gz")
  
  script:
  """
  zcat $forward | gzip > ${sample_id}_R1.fastq.gz
  zcat $reverse | gzip > ${sample_id}_R2.fastq.gz
  """
}