main.nf

version = "1.0"
container_url = "xgrand/r-bolero:${version}"

params.start_position_counts_out =""
process start_position_individuals{
  container = "${container_url}"
  label "small_mem_mono_cpus"
  tag "start positions"
  if (params.start_position_counts_out != "") {
    publishDir "results/${params.start_position_counts_out}", mode: 'copy'
  }
  input:
    path(start_position_counts)

  output:
    path("Rplots.pdf")
    path("*.png")
    path("Count_reads_per_promoter.tsv")
    path("classification_of_reads_per_RNA.txt"), emit: classification_of_reads

  script:
    """
    Rscript /Start_positions.R -i ${start_position_counts}
    """
}