epmc_ontology_annotator/nextflow.config at dev · EBISPOT/epmc_ontology_annotator · GitHub

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/*
 * =============================================================
 *  EPMC Ontology Annotator – Nextflow Configuration
 * =============================================================
 */

// --------------- Default parameters ---------------

params {
    input_dir      = null
    tagger_db      = null
    outdir         = 'results'

    ontologies     = null   // e.g. 'ecto,hpo,mondo' — null keeps all
    min_label_len  = 6
    delimiters     = " ,.;:!?()[]{}\"'/\\\t\n-+="
    progress       = 100000

    db_name        = 'epmc_tags.sqlite'
}

// --------------- Execution profiles ---------------

profiles {

    standard {
        process.executor = 'local'
    }

    docker {
        docker.enabled = true
        process.executor = 'local'
    }

    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        singularity.cacheDir   = "${projectDir}/singularity_cache"
        process.executor = 'local'
    }

    slurm {
        process {
            executor       = 'slurm'
            queue          = 'standard'
            clusterOptions = ''

            withName: 'TAG_CHUNK' {
                memory = '6 GB'
                cpus   = 1
                time   = '6h'
            }
            withName: 'LOAD_SQLITE' {
                memory = '16 GB'
                cpus   = 1
                time   = '2h'
            }
            withName: 'SUMMARISE' {
                memory = '4 GB'
                cpus   = 1
                time   = '30m'
            }
        }
    }

    lsf {
        process {
            executor = 'lsf'

            withName: 'TAG_CHUNK' {
                memory = '6 GB'
                cpus   = 1
                time   = '6h'
            }
            withName: 'LOAD_SQLITE' {
                memory = '16 GB'
                cpus   = 1
                time   = '2h'
            }
            withName: 'SUMMARISE' {
                memory = '4 GB'
                cpus   = 1
                time   = '30m'
            }
        }
    }

    // Codon / EBI cluster specifics
    codon {
        process {
            executor       = 'slurm'
            queue          = 'standard'

            withName: 'TAG_CHUNK' {
                memory = '6 GB'
                cpus   = 1
                time   = '6h'
            }
            withName: 'LOAD_SQLITE' {
                memory = '16 GB'
                cpus   = 1
                time   = '2h'
            }
            withName: 'SUMMARISE' {
                memory = '4 GB'
                cpus   = 1
                time   = '30m'
            }
        }
    }
}

// --------------- Process defaults ---------------

process {
    errorStrategy = 'retry'
    maxRetries    = 2
    container     = 'ghcr.io/ebispot/epmc_ontology_annotator:dev'
}

// --------------- Manifest ---------------

manifest {
    name            = 'epmc-ontology-annotator'
    author          = 'James McLaughlin'
    description     = 'Annotate EuropePMC abstracts with ontology terms using ols_text_tagger'
    mainScript      = 'main.nf'
    nextflowVersion = '>=23.04'
    version         = '1.0.0'
}

// --------------- Reports and tracing ---------------

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

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

trace {
    enabled   = true
    file      = "${params.outdir}/trace.txt"
    overwrite = true
    fields    = 'task_id,hash,native_id,name,status,exit,realtime,cpus,memory,%cpu,%mem,rss,peak_rss'
}

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