immunebuilder/nextflow.config

// Manifest for Nextflow metadata
manifest {
    name = 'ImmuneBuilder-Nextflow'
    author = 'Olamide'
    homePage = 'https://trs-gitea.cluster.omic.ai/omic/immunebuilder'
    description = 'Nextflow pipeline for ImmuneBuilder - Deep-Learning models for predicting structures of immune proteins (antibodies, nanobodies, TCRs)'
    mainScript = 'main.nf'
    version = '1.2.0'
}

// Global default parameters
params {
    fasta = "s3://omic/eureka/immunebuilder/antibody_test.fasta"
    outdir = "s3://omic/eureka/immunebuilder/output"
    mode = 'antibody'
    verbose = true
    original_weights = false
}

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

// Process configurations
process {
    cpus = 4
    memory = '16 GB'
    time = '2h'

    withName: 'ABODYBUILDER2' {
        cpus = 4
        memory = '16 GB'
    }

    withName: 'NANOBODYBUILDER2' {
        cpus = 4
        memory = '16 GB'
    }

    withName: 'TCRBUILDER2' {
        cpus = 4
        memory = '16 GB'
    }
}

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

// Profile configurations
profiles {
    standard {
        docker.enabled = true
    }

    gpu {
        docker.enabled = true
        docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
        process {
            containerOptions = '--rm --gpus all -v /mnt:/mnt'
        }
    }

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

    conda {
        conda.enabled = true
        docker.enabled = false
    }
}

// Logging and reporting
timeline {
    enabled = true
    file = "${params.outdir}/pipeline_info/timeline.html"
    overwrite = true
}

report {
    enabled = true
    file = "${params.outdir}/pipeline_info/report.html"
    overwrite = true
}

trace {
    enabled = true
    file = "${params.outdir}/pipeline_info/trace.txt"
    overwrite = true
}

dag {
    enabled = true
    file = "${params.outdir}/pipeline_info/dag.html"
    overwrite = true
}