// Manifest for Nextflow metadata
manifest {
    name = 'RoseTTAFold-All-Atom'
    author = 'Baker Laboratory'
    homePage = 'https://github.com/baker-laboratory/RoseTTAFold-All-Atom'
    description = 'Nextflow pipeline for RoseTTAFold-All-Atom biomolecular structure prediction'
    mainScript = 'main.nf'
    version = '1.0.0'
}

// Global default parameters
params {
    // Input files
    protein_fasta = "s3://omic/eureka/rosettafold-all-atom/input/protein.fasta"
    na_fasta = ""
    na_type = "dna"
    sm_file = ""
    sm_type = "sdf"
    covale_inputs = ""

    // Output
    outdir = "s3://omic/eureka/rosettafold-all-atom/output"
    job_name = "rfaa_prediction"

    // Model settings
    max_cycle = 4

    // Database paths
    db_uniref30 = "/mnt/databases/UniRef30_2020_06"
    db_bfd = "/mnt/databases/bfd"
    db_pdb100 = "/mnt/databases/pdb100_2021Mar03"
    weights = "/mnt/databases/RFAA_paper_weights.pt"
}

// Profiles
profiles {
    standard {
        docker {
            enabled = true
            temp = 'auto'
            runOptions = '--gpus all -v /mnt:/mnt'
        }
    }

    k8s {
        process {
            executor = 'k8s'
            container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
        }
        docker {
            enabled = true
        }
        k8s {
            storageClaimName = 'eureka-pvc'
            storageMountPath = '/omic/eureka'
        }
    }

    k8s_gpu {
        process {
            executor = 'k8s'
            container = 'harbor.cluster.omic.ai/omic/rosettafold-all-atom:latest'
            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
            accelerator = [request: 1, type: 'nvidia.com/gpu']
        }
        docker {
            enabled = true
        }
        k8s {
            storageClaimName = 'eureka-pvc'
            storageMountPath = '/omic/eureka'
        }
    }
}

// Process configurations
process {
    cpus = 8
    memory = '64 GB'
}