#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Parameters
params.pdb = '/omic/eureka/Pocketminer/1HSG.pdb'
params.outdir = '/omic/eureka/Pocketminer/output'
params.model_path = '/workspace/gvp/models/pocketminer'
params.debug = false

// Process definition
process POCKETMINER {
    container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
    publishDir params.outdir, mode: 'copy'
    stageInMode 'copy'

    input:
    path pdb_file

    output:
    path "*-preds.npy", emit: predictions_npy
    path "*-predictions.txt", emit: predictions_txt
    path "*-summary.json", emit: summary
    path "*_X.npy", optional: true, emit: features_debug
    path "*_S.npy", optional: true, emit: sequence_debug
    path "*_mask.npy", optional: true, emit: mask_debug

    script:
    def pdb_basename = pdb_file.baseName
    def debug_flag = params.debug ? '--debug' : ''
    """
    python /workspace/entrypoint.py \\
        --pdb ${pdb_file} \\
        --output-folder . \\
        --output-name ${pdb_basename} \\
        --model-path ${params.model_path} \\
        ${debug_flag}
    """
}

// Workflow
workflow {
    POCKETMINER(Channel.of(file(params.pdb)))
}