TrESFlow/nextflow.config at main · CSOgroup/TrESFlow · GitHub

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// nf-core/tools caches `nextflow config -flat` output by hashing this file and
// main.nf. Keep this file as the source of truth for repository metadata.
nextflow.enable.dsl = 2

manifest {
    name            = 'nf-core/tres'
    description     = 'Repo-owned Nextflow DSL2 implementation of the TrES core RNA and DNA workflows'
    homePage        = 'https://github.com/nf-core/tres'
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '>=24.10.0'
    version         = '0.1.0dev'
    contributors    = [
        [
            name        : 'Ahrmad Annan',
            affiliation : '',
            email       : '',
            github      : '',
            contribution: ['author'],
            orcid       : ''
        ],
        [
            name        : 'Nikita Miroshnichenko',
            affiliation : '',
            email       : '',
            github      : '',
            contribution: ['author', 'maintainer'],
            orcid       : ''
        ],
    ]
}

params {
    outdir       = null
    samplesheet  = null
    publish_dir_mode = 'copy'
    config_profile_name = null
    config_profile_description = null
    custom_config_version = 'master'
    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"

    // Repo-owned core runtime scripts
    core_scripts_dir = null

    // Barcode defaults kept out of the user-facing YAML contract
    barcode_defaults = [
        rna: [
            sample: [
                bc_len            : 4,
                bc_start          : 0,
                hd                : 1,
                tag               : 'SB',
                first_pass        : 'first_pass',
                reverse_complement: true,
            ],
            umi: [
                bc_len  : 10,
                bc_start: 4,
                tag     : 'UM',
            ],
            cell: [
                bc_len: 8,
                hd    : 1,
                tag   : 'CB',
            ],
        ],
        dna: [
            sample: [
                bc_len            : 4,
                bc_start          : 14,
                hd                : 1,
                tag               : 'SB',
                first_pass        : 'first_pass',
                reverse_complement: true,
            ],
            modality: [
                bc_len            : 8,
                bc_start          : 18,
                hd                : 1,
                tag               : 'MO',
                first_pass        : 'not_first_pass',
                reverse_complement: true,
            ],
            cell: [
                bc_len: 8,
                hd    : 1,
                tag   : 'CB',
            ],
        ],
    ]

    // Executor budget
    max_cpus = 64
    cleanup_work = true
    tagging_cpus = 4
    tagging_memory = '32 GB'
    helper_cpus = 4
    rna_starsolo_cpus = 16
    dna_align_cpus = 16
    coverage_cpus = 8
}

includeConfig 'conf/base.config'

profiles {
    standard {
    }
    test {
        includeConfig 'conf/test.config'
    }
    test_full {
        includeConfig 'conf/test_full.config'
    }
}

// Load nf-core custom profiles from different institutions
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

cleanup = (params.cleanup_work instanceof Boolean) ? params.cleanup_work : params.cleanup_work.toString().toBoolean()

executor {
    cpus = params.max_cpus as int
}