nextflow.enable.dsl=2

process CORTO {
  memory 1.GB

  container "${params.container_corto}"
  containerOptions "${params.containerOptions}"
  publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
  // debug true
  // maxForks 1
  stageInMode 'copy'

  input:
    path TPM
    path regulon
    // path TPM_ref

  // Define output channels
  output:
    path "*_metabolome.csv", emit: csv_metabol

  script:
    """
    #!/usr/bin/Rscript
    library(corto)
    library(data.table)

    TPM <- as.matrix(fread("$TPM"),rownames=1)
    #TPM_ref <- as.matrix(fread("TPM_ref"),rownames=1) #dollar sign is missing

    #try normalization; dont use
    #TPM <- scale(TPM)
    #TPM_log2 = log2(TPM + 1)

    load("$regulon")
    
    predicted<-mra(TPM, regulon=regulon)

    #use this if we want to compare patients and reference TPM, data formet output is not csv -> work on data saving if needed
    #predicted<-mra(TPM, path TPM_ref, regulon=regulon)

    name = strsplit(strsplit("$TPM", split = "/")[[1]][length(strsplit("$TPM", split = "/")[[1]])],  split = "_TPM.csv")[[1]][1]
    name = paste(name, "_metabolome.csv", sep="")
    write.csv(predicted, name)
    """
}