nextflow.enable.dsl=2

// Default parameters (override via -params-file). Listed here to document every
// parameter this workflow needs. Values copied from a representative job
// (R06-ivan-gabe-bioprops-rerun/J17-bioprops/params.json).
params.container_biotransformer = "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5"
params.container_conplex        = "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3"
params.container_tissue         = "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.1.0"
params.container_preprocess     = "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17"
params.container_mass_screen    = "harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1"
params.container_chembl         = "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0"
params.containerOptions         = "--rm"
params.project_name             = "bioprops-gabe-run-drug-target"
params.outdir                   = "/mnt/dreamdock-data/digital_trials/runs/R06-ivan-gabe-bioprops-rerun/J17-bioprops/output"
params.ligands                  = "/mnt/dreamdock-data/digital_trials/input/gabe-run/input/ligand-drug-target"
params.metabolites              = "/mnt/dreamdock-data/digital_trials/input/gabe-run/output/drug-target/screening"
params.conplex_dir              = "/mnt/dreamdock-data/digital_trials/input/gabe-run/output/drug-target/conplex"

include { BIO_METRICS } from './main_tissue.nf'

workflow {
    lig_ch  = Channel.fromPath("${params.ligands}/*.csv")
                     .map { [it.simpleName, it] }
    met_ch  = Channel.fromPath("${params.metabolites}/*_out.txt")
                     .map { f -> [f.simpleName.replaceAll(/_out$/, ''), f] }
    drug_ch = Channel.fromPath("${params.conplex_dir}/*_patient_0_drug_scores.tsv")
                     .map { f -> [f.simpleName.replaceAll(/_patient_0_drug_scores$/, ''), f] }
    int_ch  = Channel.fromPath("${params.conplex_dir}/*_patient_0_significant_interactions.tsv")
                     .map { f -> [f.simpleName.replaceAll(/_patient_0_significant_interactions$/, ''), f] }

    biometric_ch = lig_ch.join(met_ch).join(drug_ch).join(int_ch)
    BIO_METRICS(biometric_ch)
}