nextflow.enable.dsl=2

//BIOTRANSFORMER
params.container_biotransformer = 'biotransformer:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
params.project_name = 'test'
params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'

//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented

//CONPLEX
params.container_conplex = 'conplex_dig_pat:latest'
params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input'
params.threshold = 0.8 //0.5 //0.7 
params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
params.protein_network_threshold = 0.95

//TISSUE DISTRIBUTION
params.container_tissue = 'tissue:latest'

//BIOTRANSFORMER
include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
//CONPLEX
include { CONPLEX } from './main_conplex.nf'
include { NETWORK_ENRICHMENT } from './main_conplex.nf'
//TISSUE_DISTRIBUTION
include { TISSUE_DISTRIBUTION } from './main_tissue.nf'

workflow {
    //BIOTRANSFORMER
    lig_ch = Channel.fromPath("${params.ligands}/*.csv")
    switch (params.mode) {
        case 'SUPER':
            SUPER_TRANSFORMER(lig_ch)
            break
        case 'HUMAN':
            HUMAN_TRANSFORMER(lig_ch)
            break
        case 'MASS':
            METABOLITES_BY_MASS(lig_ch)
            break
        case 'ORDERED':
            ORDERED_SEQUENCE(lig_ch)
            break
        default:
            println("Invalid mode specified: ${params.mode}")
    }
    GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
    //CONPLEX
    pat_fasta = Channel.fromPath("${params.mutated_protein_fasta}/*.fasta")
    CONPLEX(lig_ch, GET_FINAL_METABOLITES.out, pat_fasta)
    NETWORK_ENRICHMENT(CONPLEX.out.interactions)
    //TISSUE DISTRIBUTION
    TISSUE_DISTRIBUTION(CONPLEX.out.interactions)
}