BioXend/nextflow.config at devel · zmahnoor14/BioXend · GitHub

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/*
 * BioXend — nextflow.config
 * MIX-MB ChEMBL Submission Pipeline
 */

manifest {
    name            = 'BioXend'
    author          = 'Mahnoor Zulfiqar & Eleonora Mastrorilli (EMBL)'
    description     = 'MIX-MB ChEMBL submission file generator'
    mainScript      = 'main.nf'
    nextflowVersion = '>=22.10.0'
    version         = '0.1.0'
}

// ─────────────────────────────────────────────────────────────────────────────
// Default parameters (can be overridden on the command line)
// ─────────────────────────────────────────────────────────────────────────────

params {
    input            = null
    ridx             = null
    prefix           = "CIDX"
    xenobiotic_class = "xenobiotic compound"
    dose             = ""
    dose_units       = "uM"
    dose_comments    = ""
    outdir           = "${projectDir}/results"
    strict           = false
    help             = false
}

// ─────────────────────────────────────────────────────────────────────────────
// Process defaults
// ─────────────────────────────────────────────────────────────────────────────

process {
    errorStrategy = 'retry'
    maxRetries    = 1

    withName: 'GENERATE_REFERENCE'   { memory = '2 GB'; cpus = 1 }
    withName: 'GENERATE_CHEMICALS'   { memory = '4 GB'; cpus = 2 }
    withName: 'GENERATE_ASSAY'       { memory = '2 GB'; cpus = 1 }
    withName: 'GENERATE_ASSAY_PARAM' { memory = '2 GB'; cpus = 1 }
    withName: 'GENERATE_ACTIVITY'    { memory = '2 GB'; cpus = 1 }
}

// ─────────────────────────────────────────────────────────────────────────────
// Profiles
// ─────────────────────────────────────────────────────────────────────────────

profiles {

    // Default: local execution, no container
    standard {
        process.executor = 'local'
    }

    // Conda — recommended for local use
    conda {
        conda.enabled     = true
        conda.useMamba    = false
        process.executor  = 'local'
    }

    // Docker
    docker {
        docker.enabled    = true
        docker.runOptions = '-u $(id -u):$(id -g)'
        process {
            container = 'bioxend:latest'
        }
    }

    // Singularity
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        process {
            container = 'docker://bioxend:latest'
        }
    }

    // SLURM HPC cluster
    slurm {
        process.executor     = 'slurm'
        process.queue        = 'batch'
        process.clusterOptions = '--qos=normal'
        conda.enabled        = true
    }
}

// ─────────────────────────────────────────────────────────────────────────────
// Conda settings
// ─────────────────────────────────────────────────────────────────────────────

conda {
    createTimeout = '30 min'
    cacheDir      = "${HOME}/.nextflow/conda"
}

// ─────────────────────────────────────────────────────────────────────────────
// Reporting (HTML reports written to outdir/reports/)
// ─────────────────────────────────────────────────────────────────────────────

report {
    enabled = true
    file    = "${params.outdir}/reports/execution_report.html"
}

timeline {
    enabled = true
    file    = "${params.outdir}/reports/execution_timeline.html"
}

trace {
    enabled = true
    file    = "${params.outdir}/reports/execution_trace.txt"
}