// =============================================================================
// PRODIGY Nextflow Pipeline Configuration
// Protein binding affinity prediction from structural data
// =============================================================================

// Manifest for Nextflow metadata
manifest {
    name = 'PRODIGY-Nextflow'
    author = 'Olamide'
    homePage = 'https://trs-gitea.cluster.omic.ai/omic/prodigy'
    description = 'Nextflow pipeline for PRODIGY - Protein binding affinity prediction based on intermolecular contacts'
    mainScript = 'main.nf'
    version = '2.4.0'
}

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

// Container configurations
docker {
    enabled = true
    runOptions = '-u $(id -u):$(id -g)'
}

// Process configurations
process {
    cpus = 1
    memory = '4 GB'
    container = 'harbor.cluster.omic.ai/omic/prodigy:latest'
}

// Execution configurations
executor {
    $local {
        cpus = 4
        memory = '8 GB'
    }
}

// Profiles for different execution environments
profiles {
    standard {
        docker.enabled = true
    }

    k8s {
        docker.enabled = true
        process.container = 'harbor.cluster.omic.ai/omic/prodigy:latest'
    }

    k8s_gpu {
        docker.enabled = true
        process.container = 'harbor.cluster.omic.ai/omic/prodigy:latest'
    }

    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        docker.enabled = false
    }
}