main.nf

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

params.rna_count_out = ""
process rna_count{
  container = "${container_url}"
  label "small_mem_mono_cpus"
  tag "RNA quantification"
  if (params.rna_count_out != "") {
    publishDir "results/${params.rna_count_out}", mode: 'copy'
  }

  input:
    path(spvariants)
    path(classification)

  output:
    path("*.csv")
    path("*.pdf")
    path("*.png")

  script:
    """
    Rscript /HBV_RNAs_count.R -s ${spvariants} -c ${classification}
    """
}