nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/proteinannotator Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input options
    input = null

    // QC
    skip_preprocessing            = false
    min_seq_length                = 30
    max_seq_length                = 5000
    remove_duplicates_on_sequence = false

    // Domain annotation
    skip_pfam               = false
    pfam_db                 = null
    pfam_latest_link        = "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
    skip_funfam             = false
    funfam_db               = null
    funfam_latest_link      = "https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz"
    skip_nmpfams            = false
    nmpfams_db              = null
    nmpfams_latest_link     = "https://pavlopoulos-lab.org/envofams/databases/hmmer/nmpfamsdb.hmm.gz"
    skip_metagroot          = false
    metagroot_db            = null
    metagroot_latest_link   = "https://pavlopoulos-lab.org/envofams/databases/hmmer/metagroot.hmm.gz"
    hmmsearch_evalue_cutoff = 0.001

    // Functional annotation
    skip_interproscan          = false
    interproscan_db_url        = "https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz"
    interproscan_db            = null
    interproscan_applications  = 'Hamap,PANTHER,PIRSF,TIGRFAM,sfld'
    interproscan_enableprecalc = false

    // Secondary structure prediction (s4pred)
    skip_s4pred   = false
    s4pred_outfmt = 'ss2'  // ["ss2", "fas", "horiz"]

    // MultiQC options
    multiqc_config = null
    multiqc_title = null
    multiqc_logo = null
    max_multiqc_email_size = '25.MB'
    multiqc_methods_description = null

    // Boilerplate options
    outdir                       = null
    publish_dir_mode             = 'copy'
    email                        = null
    email_on_fail                = null
    plaintext_email              = false
    monochrome_logs              = false
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')

    // Config options
    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}"
    config_profile_contact     = null
    config_profile_url         = null
    modules_testdata_base_path = null

    // Schema validation default options
    validate_params = true
}

// Backwards compatibility for publishDir syntax
outputDir = params.outdir
workflow.output.mode = params.publish_dir_mode

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug {
        dumpHashes = true
        process.beforeScript = 'echo $HOSTNAME'
        cleanup = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled = true
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        conda.channels = ['conda-forge', 'bioconda']
        apptainer.enabled = false
    }
    mamba {
        conda.enabled = true
        conda.useMamba = true
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    docker {
        docker.enabled = true
        conda.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
        docker.runOptions = '-u $(id -u):$(id -g)'
    }
    arm64 {
        process.arch            = 'arm64'
        // TODO https://github.com/nf-core/modules/issues/6694
        // For now if you're using arm64 you have to use wave for the sake of the maintainers
        // wave profile
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    emulate_amd64 {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        conda.enabled = false
        docker.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    podman {
        podman.enabled = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    shifter {
        shifter.enabled = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    charliecloud {
        charliecloud.enabled = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        apptainer.enabled = false
    }
    apptainer {
        apptainer.enabled = true
        apptainer.autoMounts = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
    }
    wave {
        apptainer.ociAutoPull = true
        singularity.ociAutoPull = true
        wave.enabled = true
        wave.freeze = true
        wave.strategy = 'conda,container'
    }
    gpu {
        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions    = '--nv'
        singularity.runOptions  = '--nv'
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}

// Load nf-core custom profiles from different institutions

// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/proteinannotator 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 nf-core/proteinannotator custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/proteinannotator.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'



// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER = "/.Rprofile"
    R_ENVIRON_USER = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// Set bash options
process.shell = [
    "bash",
    "-C",
    "-e",
    "-u",
    "-o",
    "pipefail",
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

timeline {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
    enabled = true
    file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
    enabled = true
    file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
    name            = 'nf-core/proteinannotator'
    contributors    = [
        [
            name: 'Olga Botvinnik',
            affiliation: 'Seanome, San Francisco, CA, USA',
            email: 'olga@seanome.org',
            github: 'olgabot',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: 'https://orcid.org/0000-0003-4412-7970'
        ],
        [
            name: 'Michael L Heuer',
            affiliation: """Network.bio, New York, NY, USA""",
            email: '',
            github: '@heuermh',
            contribution: ['contributor'],
            orcid: 'https://orcid.org/0000-0002-9052-6000'
        ],
        [
            name: 'Evangelos Karatzas',
            affiliation: 'EMBL-EBI',
            email: 'vangelis@ebi.ac.uk',
            github: 'https://github.com/vagkaratzas',
            contribution: ['maintainer'],
            orcid: '0000-0001-9132-8981'
        ]
    ]
    homePage        = 'https://github.com/nf-core/proteinannotator'
    description     = """Generation of sequence-level annotations for amino acid sequences"""
    mainScript      = 'main.nf'
    defaultBranch   = 'master'
    nextflowVersion = '!>=25.10.4'
    version         = '1.1.0'
    doi             = '10.5281/zenodo.18547735'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.6.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs = params.monochrome_logs
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'