//
// Pipeline configuration for nf-carafe-ai-ms
//
// This is a template configuration file. Edit the values below to match your
// data and system. For a complete description of all parameters, see:
// https://nf-carafe-ai-ms.readthedocs.io/en/latest/workflow_parameters.html
//
// Questions, comments, or bug reports: Michael Riffle <mriffle@uw.edu>
//

params {

    //
    // ── Input Spectra ────────────────────────────────────────────────────
    //
    // Specify EITHER spectra_file (for a single file) OR spectra_dir
    // (for a directory of files), but not both.
    //
    // Supported file types: .raw (Thermo), .mzML, .d (Bruker), .d.zip (Bruker zipped)
    // Paths may be local, S3 URIs, or PanoramaWeb WebDAV URLs.
    // Note: Bruker .d directories cannot be downloaded from PanoramaWeb; use .d.zip instead.
    //

    spectra_file = '/path/to/file.raw'

    //spectra_dir = '/path/to/spectra_dir'
    //spectra_dir_glob = '*.raw'       // glob pattern to select files from spectra_dir (default: '*.raw')

    //
    // ── Output ───────────────────────────────────────────────────────────
    //

    // Format of the output spectral library: 'diann' (TSV) or 'encyclopedia' (DLIB)
    output_format = 'diann'

    //
    // ── DIA-NN Settings ──────────────────────────────────────────────────
    //
    // DIA-NN is used to generate peptide identifications as input to Carafe.
    // If you already have DIA-NN results, set peptide_results_file to skip
    // running DIA-NN.
    //

    // Path to pre-computed DIA-NN results (.tsv). If set, DIA-NN will be skipped.
    peptide_results_file = null

    // FASTA file for DIA-NN. If not set, carafe_fasta_file will be used.
    diann_fasta_file = null

    // Command line parameters for DIA-NN.
    diann_params = '--unimod4 --qvalue 0.01 --cut \'K*,R*,!*P\' --reanalyse --smart-profiling'

    //
    // ── Carafe Settings ──────────────────────────────────────────────────
    //
    // Carafe uses AI to generate an experiment-specific spectral library
    // from the FASTA and DIA-NN results.
    //

    // FASTA file for Carafe (required)
    carafe_fasta_file = null

    // Carafe command line options. The defaults in the workflow are sensible
    // for most DIA searches. See: https://github.com/Noble-Lab/Carafe
    // Do not set: -mode, -varMod, -maxVar, -ms, -db, -i, -se, -lf_type, -device
    //cli_options = '-fdr 0.01 -ptm_site_prob 0.75 ...'

    // Variable modifications to include in the spectral library.
    // Set to true to enable. Both may be enabled at once.
    //include_phosphorylation = true
    //include_oxidized_methionine = true

    // Max variable modifications allowed per peptide. Ignored if no variable
    // modifications are enabled.
    //max_mod_option = '-maxVar 1'

    //
    // ── msconvert Settings ───────────────────────────────────────────────
    //
    // These settings apply when starting from Thermo .raw files.
    //

    msconvert.do_demultiplex = true
    msconvert.do_simasspectra = true

    //
    // ── Container Image Overrides ────────────────────────────────────────
    //
    // Override the default container images used by the workflow. This is
    // useful for using a newer version of DIA-NN. See the documentation
    // for how to build a custom DIA-NN Docker image:
    // https://nf-carafe-ai-ms.readthedocs.io/en/latest/custom_diann.html
    //
    //images.diann = 'diann:2.3.2'

    //
    // ── Email Notification ───────────────────────────────────────────────
    //
    // Set an email address to receive a notification when the workflow completes.
    // Requires mail server configuration below.
    //
    //email = 'your@email.com'
}

//
// ── System Resources ─────────────────────────────────────────────────────
//
// Adjust these to match the resources available on your system.
// These only need to be set once per system, not per run.
//

profiles {

    standard {
        params.max_memory = '8.GB'
        params.max_cpus = 4
        params.max_time = '240.h'

        params.mzml_cache_directory = './mzml_cache'
        params.panorama_cache_directory = './raw_cache'
    }
}

//
// ── Mail Server (optional) ───────────────────────────────────────────────
//
// Configure these settings to enable email notifications on workflow
// completion. You may need to contact your IT department for the
// correct SMTP settings.
//

mail {
    from = 'address@host.com'
    smtp.host = 'smtp.host.com'
    smtp.port = 587
    smtp.user = 'smtp_user'
    smtp.password = 'smtp_password'
    smtp.auth = true
    smtp.starttls.enable = true
    smtp.starttls.required = false
    mail.smtp.ssl.protocols = 'TLSv1.2'
}