// Manifest for Nextflow metadata
manifest {
    name = 'LigandMPNN-Nextflow'
    author = 'Generated from LigandMPNN repository'
    homePage = 'https://github.com/dauparas/LigandMPNN'
    description = 'Nextflow pipeline for LigandMPNN - Protein sequence design with ligand context'
    mainScript = 'main.nf'
    version = '1.0.0'
}

// Global default parameters
params {
    pdb = "s3://omic/eureka/ligandmpnn/1BC8"
    outdir = "s3://omic/eureka/ligandmpnn/output"
    model_type = "ligand_mpnn"
    temperature = 0.1
    seed = 111
    batch_size = 1
    number_of_batches = 1
    chains_to_design = ""
    fixed_residues = ""
}

// Container configurations
docker {
    enabled = true
    runOptions = '--gpus all'
}

// Process configurations
process {
    cpus = 4
    memory = '16 GB'
}

// Execution configurations
executor {
    $local {
        cpus = 8
        memory = '32 GB'
    }
}

// Kubernetes profile for WES execution
profiles {
    k8s {
        docker.enabled = false
        process.container = 'harbor.cluster.omic.ai/omic/ligandmpnn:v2'
    }
    k8s_gpu {
        docker.enabled = false
        process.container = 'harbor.cluster.omic.ai/omic/ligandmpnn:v2'
    }
}