#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Pipeline 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 POCKETMINER {
    container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
    publishDir params.outdir, mode: 'copy'

    input:
        val pdb_path

    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
        path "run.log", emit: log

    script:
        def pdb_basename = file(pdb_path).baseName
        def debug_flag = params.debug ? '--debug' : ''
        """
        touch run.log

        echo "=== Debugging PVC mount ===" | tee -a run.log
        echo "Input path: ${pdb_path}" | tee -a run.log
        ls -la /omic/eureka/ 2>&1 | head -20 | tee -a run.log
        ls -la /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
        echo "=== End Debug ===" | tee -a run.log

        if [ ! -f "${pdb_path}" ]; then
            echo "ERROR: PDB file not found at ${pdb_path}" | tee -a run.log
            echo "Available files in /omic/eureka/Pocketminer/:" | tee -a run.log
            ls /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
            exit 1
        fi

        cp "${pdb_path}" input.pdb

        python /workspace/entrypoint.py \\
            --pdb input.pdb \\
            --output-folder . \\
            --output-name ${pdb_basename} \\
            --model-path ${params.model_path} \\
            ${debug_flag} 2>&1 | tee -a run.log

        echo "Pipeline completed successfully" | tee -a run.log
        """
}

workflow {
    POCKETMINER(params.pdb)
}