#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Default parameters
params.pdb = 's3://omic/eureka/prodigy/input/*.pdb'
params.outdir = 's3://omic/eureka/prodigy/output'
params.distance_cutoff = 5.5
params.acc_threshold = 0.05
params.temperature = 25.0
params.selection = ''
params.contact_list = false
params.pymol_selection = false
params.quiet = false

// =============================================================================
// Process: PRODIGY
// Predicts binding affinity using intermolecular contacts
// =============================================================================

process PRODIGY {
    container 'harbor.cluster.omic.ai/omic/prodigy:latest'
    publishDir params.outdir, mode: 'copy'
    stageInMode 'copy'

    input:
        path pdb

    output:
        path "${pdb.baseName}_prodigy.txt", emit: results
        path "${pdb.baseName}_contacts.txt", optional: true, emit: contacts
        path "${pdb.baseName}_interface.pml", optional: true, emit: pymol

    script:
        """
        prodigy \\
            ${pdb} \\
            --distance-cutoff ${params.distance_cutoff} \\
            --acc-threshold ${params.acc_threshold} \\
            --temperature ${params.temperature} \\
            ${params.selection ? '--selection ' + params.selection : ''} \\
            ${params.contact_list ? '--contact_list' : ''} \\
            ${params.pymol_selection ? '--pymol_selection' : ''} \\
            ${params.quiet ? '--quiet' : ''} \\
            2>&1 | tee ${pdb.baseName}_prodigy.txt

        # Rename contact list file if generated
        if [ -f "${pdb.baseName}.contacts" ]; then
            mv ${pdb.baseName}.contacts ${pdb.baseName}_contacts.txt
        fi

        # Rename PyMOL script if generated
        if [ -f "${pdb.baseName}.pml" ]; then
            mv ${pdb.baseName}.pml ${pdb.baseName}_interface.pml
        fi
        """
}

// =============================================================================
// Workflow
// =============================================================================

workflow {
    // Validate input
    if (!params.pdb) {
        error "ERROR: Please provide input PDB file(s) using --pdb parameter"
    }

    // Create input channel
    pdb_ch = Channel.fromPath(params.pdb, checkIfExists: true)

    // Run PRODIGY
    PRODIGY(pdb_ch)
}