nextflow.enable.dsl=2


process TISSUE_DISTRIBUTION {
    memory { params.tissue_initial_memory.toInteger().GB + (task.attempt - 1) * params.tissue_growth_memory.toInteger().GB }

    container "${params.container_tissue}"
    // containerOptions "${params.containerOptions}"
    publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
    // // Temporarily disabled debug prints
    // debug true

    errorStrategy { task.attempt <= params.tissue_max_retries.toInteger() ? 'retry' : params.tissue_fail_action }
    maxRetries params.tissue_max_retries.toInteger()

    input:
     path interaction

    output:
     path "*tissue_distribution.tsv", emit: tissue_dist

    script:
    """
    # . activate tissue
    python /home/omic/drug_tissue_distribution.py --file_name ${interaction}
    """
}

process BIO_METRICS {
    memory { params.bio_initial_memory.toInteger().GB + (task.attempt - 1) * params.bio_growth_memory.toInteger().GB }

    container "${params.container_tissue}"
    // containerOptions "${params.containerOptions}"
    publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
    // debug true

    errorStrategy { task.attempt <= params.bio_max_retries.toInteger() ? 'retry' : params.bio_fail_action }
    maxRetries params.bio_max_retries.toInteger()

    input:
      tuple (
        val(id),
        path( target),
        path( metabolites),
        path( conplex_drug),
        path( conplex_all_interactions),
     )

    output:
     path "*_biological_properties.tsv", emit: bio_prop

    script:
    """
    # . activate tissue
    python /home/omic/digital_patient_extract_metrics.py --metabolites ${metabolites} --conplex_all_interactions ${conplex_all_interactions} --conplex_drug ${conplex_drug} --target ${target}
    """
}