#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Parameters
params.TPM = '/omic/eureka/corto/20002_1289_female_patient_0_TPM.csv'
params.regulon = '/omic/eureka/corto/regulon.rda'
params.outdir = '/omic/eureka/corto/output'

process CORTO {
  container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
  publishDir params.outdir, mode: 'copy'
  debug true

  input:
    path TPM
    path regulon

  output:
    path "*_metabolome.csv", emit: csv_metabol

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

    TPM <- as.matrix(fread("$TPM"),rownames=1)

    load("$regulon")

    predicted<-mra(TPM, 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)
    """
}

workflow {
  CORTO(Channel.of(file(params.TPM)), Channel.of(file(params.regulon)))
}