sramic/nextflow.config at main · microbemarsh/sramic · GitHub

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manifest {
    name = 'sramic'
    author = 'sramic contributors'
    homePage = 'https://github.com/microbemarsh/sramic'
    description = 'Metadata-first SRA discovery, filtering, and selective genomic-data retrieval'
    mainScript = 'main.nf'
    nextflowVersion = '>=26.04.6'
    version = '0.4.0'
}

params {
    outdir = 'results'
    manifest = null
    taxid = null
    taxon_id = null
    taxon_name = null
    supplement_biosample = false
    metadata_cache = 'work/cache/metadata'
    metadata_synonyms = "${projectDir}/assets/metadata_synonyms.yaml"
    missing_value_terms = "${projectDir}/assets/missing_value_terms.txt"
    geography_validation = 'syntax'
    country_boundaries = null
    ncbi_taxdump = null
    gtdb_mapping = null
    min_metadata_score = 0
    min_geography_score = 0
    min_date_score = 0
    min_host_score = 0
    require_country = false
    require_coordinates = false
    require_collection_date = false
    require_host = false
    require_isolation_source = false
    library_strategy = null
    library_source = null
    library_selection = null
    platform = null
    instrument_model = null
    collection_year_min = null
    collection_year_max = null
    country = null
    host_tax_id = null
    max_accessions = 0
    threads = 8
    download_retries = 3
    fetch_raw_reads = false
    download_sra = false
    download_sequences = false
    estimate_download_size = false
    download_backend = 'kingfisher'
    kingfisher_annotate = false
    kingfisher_methods = 'ena-ftp,aws-http,prefetch'
    kingfisher_output_format = 'fastq.gz'
    kingfisher_download_threads = null
    kingfisher_check_md5 = true
    kingfisher_force = false
    sracha_format = 'sra'
    sracha_connections = null
    output_tsv = false
    metadata_policy_version = 'occurrence-v1'
    embedding_chunk_bases = 8192
    embedding_chunk_overlap = 512
    slurm_account = null
    slurm_qos = null
    slurm_partition = null
    slurm_email = null
}

includeConfig 'conf/base.config'

// Treat --threads as a hard CPU pool for local execution. Process requests in
// conf/base.config let Nextflow schedule independent work within that pool.
executor.$local.cpus = params.threads

profiles {
    test { includeConfig 'conf/test.config' }
    local { includeConfig 'conf/local.config' }
    slurm { includeConfig 'conf/slurm.config' }
    hipergator { includeConfig 'conf/hipergator.config' }
    conda {
        conda.enabled = true
        process.conda = "${projectDir}/environments/environment.yml"
    }
    docker {
        docker.enabled = true
        process.container = 'ghcr.io/microbemarsh/sramic:0.4.0'
    }
    apptainer {
        apptainer.enabled = true
        apptainer.autoMounts = true
        process.container = 'docker://ghcr.io/microbemarsh/sramic:0.4.0'
    }
    wave {
        wave.enabled = true
        fusion.enabled = true
    }
}

report {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_report.html"
}
timeline {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_timeline.html"
}
trace {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_trace.txt"
}
dag {
    enabled = true
    file = "${params.outdir}/pipeline_info/pipeline_dag.html"
}