if (params.transcriptome_index) {
  Channel
    .fromPath( params.transcriptome_index )
    .ifEmpty { exit 1, "Cannot find any transcriptome index file : ${params.transcriptome_index}" }
    .set { transcriptome_index }
}

/*--------------------------------------------------
  Index the transcriptome
---------------------------------------------------*/

process index {
  tag "$name"

  input:
  set val(name), file(transcriptome) from transcriptome

  output:
  file "${name}.index" into transcriptome_index

  when: !params.transcriptome_index

  script:
  """
  kallisto index -i ${name}.index ${transcriptome}
  """
}

Channel
  .fromPath(params.experiment)
  .ifEmpty { exit 1, "Cannot find experiment file : ${params.experiment}" }
  .into { experiment; experiment_to_reads }
if (params.singleEnd) {
  experiment_to_reads
    .splitCsv(skip:1)
    .map { sample_id, treatment, fastq -> [sample_id, file(fastq)] }
    .set { reads }
}
if (!params.singleEnd) {
  experiment_to_reads
    .splitCsv(skip:1)
    .map { sample_id, treatment, fastq1, fastq2 -> [sample_id, [file(fastq1), file(fastq2)]] }
    .set { reads }
}