main.nf

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

params.nanosplicer_out = ""
process junctions_nanosplicer{
  container = "${container_url}"
  label "small_mem_mono_cpus"
  tag "identification de variants d'épissage"
  if (params.nanosplicer_out != "") {
    publishDir "results/${params.nanosplicer_out}", mode: 'copy'
  }

  input:
    path(txt)
    path(csv)

  output:
    path("Rplots.pdf")
    path("JWR_check_parsed.csv")
    path("*.png")
    path("identified_SPvariants.csv"), emit: identified_SPvariants

  script:
    """
    Rscript /Junctions_NanoSplicer.R -c ${txt} -j ${csv}
    """
}