manifest {
    name = 'bioemu'
    author = 'Olamide'
    description = 'BioEmu - Biomolecular Emulator for protein structure sampling and binding energy analysis'
    mainScript = 'main.nf'
    version = '1.0.0'
}

params {
    protein1_fasta = '/omic/eureka/bioemu/input/trp_cage.fasta'
    protein2_fasta = '/omic/eureka/bioemu/input/villin_headpiece.fasta'
    complex_name = 'protein_complex'
    exp_dG = -10.0
    outdir = '/omic/eureka/bioemu/output'
    cache_dir = '/tmp/bioemu_cache'
    num_samples = 10
    batch_size = 5
    temperature = 300
    n_clusters = 5
}

profiles {
    standard {
        docker {
            enabled = true
            runOptions = '--gpus all'
        }
    }

    k8s {
        process {
            executor = 'k8s'
        }
        docker {
            enabled = true
        }
    }

    k8s_gpu {
        process {
            executor = 'k8s'
            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
            accelerator = [request: 1, type: 'nvidia.com/gpu']
        }
        docker {
            enabled = true
        }
    }
}

process {
    container = 'harbor.cluster.omic.ai/omic/bioemu:latest'
    cpus = 2
    memory = '8 GB'
}