nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    bigbio/quantmsdiann Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Workflow flags
    root_folder        = null
    local_input_type   = 'raw'
    database           = null

    // Input options and validation of sdrf files
    input                      = null
    use_ols_cache_only         = true // Use only the OLS cache for ontology validation (no network requests)

    // Tools flags
    precursor_qvalue        = 0.01   // --qvalue: precursor-level q-value threshold for main report
    matrix_qvalue           = 0.01   // --matrix-qvalue: q-value threshold for output matrices
    matrix_spec_q           = 0.05   // --matrix-spec-q: run-specific protein q-value for protein/gene matrices

    // Debug level
    pp_debug                = 0

    //// Conversion and mzml statistics flags
    reindex_mzml          = false
    mzml_statistics       = false
    mzml_features         = false
    // Convert Thermo .raw to .mzML via ThermoRawFileParser before feeding DIA-NN.
    // null = auto: convert when DIA-NN < 2.1.0 (no native Linux .raw reader),
    //              pass .raw straight through when DIA-NN >= 2.1.0.
    // Set true to force conversion, false to force native .raw (requires DIA-NN >= 2.1.0).
    mzml_convert          = null

    // PRIDE download (pridepy)
    pridepy_download         = false
    project_accession        = null       // PRIDE/PX accession for pridepy download and QPX output prefix
    pridepy_protocol         = 'globus'
    aspera_maximum_bandwidth = '1000M'

    // shared search engine parameters
    met_excision                  = true // Met-excision is enabled by default
    allowed_missed_cleavages      = 2
    precursor_mass_tolerance      = 5
    precursor_mass_tolerance_unit = 'ppm'
    variable_mods                 = 'Oxidation (M)'
    fragment_mass_tolerance       = 0.03
    fragment_mass_tolerance_unit  = 'Da'
    min_precursor_charge          = 2
    max_precursor_charge          = 4
    min_peptide_length            = 6
    max_peptide_length            = 40
    max_mods                      = 3
    min_pr_mz                     = 400
    max_pr_mz                     = 2400
    min_fr_mz                     = 100
    max_fr_mz                     = 1800

    // DIA-NN: General
    diann_version           = '1.8.1'   // Used to control version-dependent flags (e.g. --monitor-mod for 1.8.x)
    debug_level             = 3
    speclib                 = null
    extra_args              = null
    scoring_mode      = 'generic'  // Scoring mode: 'generic' (default), 'proteoforms' (variant detection, >= 2.0), 'peptidoforms' (PTM analysis)
    aa_eq                   = false  // add '--aa-eq': treat I&L, Q&E, N&D as equivalent during reannotation (essential for entrapment FDR benchmarks)
    dda                     = false  // Fallback: explicitly enable DDA when SDRF lacks acquisition method (requires DIA-NN >= 2.3.2)
    light_models            = false  // add '--light-models' for 10x faster library generation (DIA-NN >= 2.0)
    export_quant            = false  // add '--export-quant' for fragment-level parquet export (DIA-NN >= 2.0)
    site_ms1_quant          = false  // add '--site-ms1-quant' for MS1 apex PTM quantification (DIA-NN >= 2.0)

    // DIA-NN: Model fine-tuning (v2.3.2+)
    enable_fine_tuning      = false  // Enable model fine-tuning before the main analysis
    tune_n_files            = 3      // Number of files to use for the tuning search (largest/best quality recommended)
    tune_fr                 = false  // Also fine-tune the fragmentation model (quality-sensitive)
    tune_lr                 = null   // Fine-tuning learning rate (default: 0.0005)

    // DIA-NN: InfinDIA (experimental, v2.3.0+)
    enable_infin_dia        = false  // Enable InfinDIA for ultra-large search spaces
    pre_select              = null   // --pre-select N precursor limit for InfinDIA

    // Optional outputs — control which intermediate files are published
    save_speclib_tsv        = false  // Save the TSV spectral library from in-silico generation

    // DIA-NN: PTM site localization (--monitor-mod)
    enable_mod_localization  = false
    // Comma-separated modification names, e.g. 'Phospho (S),Phospho (T),Phospho (Y)'
    // or UniMod accessions, e.g. 'UniMod:21,UniMod:1'
    mod_localization         = 'Phospho (S),Phospho (T),Phospho (Y)'

    // DIA-NN: PRELIMINARY_ANALYSIS — calibration & mass accuracy
    scan_window             = 8
    scan_window_automatic   = true
    mass_acc_automatic      = true
    performance_mode        = true // add '--min-corr 2 --corr-diff 1 --time-corr-only'
    quick_mass_acc          = true
    tims_sum                = false // add '--quant-tims-sum'
    im_window               = null // add '--im-window'

    // DIA-NN: ASSEMBLE_EMPIRICAL_LIBRARY — library assembly
    skip_preliminary_analysis    = false
    random_preanalysis           = false
    random_preanalysis_seed      = 42
    empirical_assembly_ms_n      = 200

    // DIA-NN: INDIVIDUAL_ANALYSIS
    mass_acc_ms2    = 15
    mass_acc_ms1    = 15

    // DIA-NN: FINAL_QUANTIFICATION — summarization & output
    pg_level                = 2
    species_genes           = false
    normalize               = true
    report_decoys           = false
    export_xic              = false
    quantums                = false
    quantums_train_runs     = null
    quantums_sel_runs       = null
    quantums_params         = null
    use_quant               = true // add '--use-quant' to FINAL_QUANTIFICATION
    channel_run_norm        = false // add '--channel-run-norm' to FINAL_QUANTIFICATION
    channel_spec_norm       = false // add '--channel-spec-norm' to FINAL_QUANTIFICATION

    // QPX export (experimental, 2.1.0)
    enable_qpx_export        = false      // Export DIA-NN output to QPX Parquet + MuData (.h5mu); requires --project_accession

    // pmultiqc options
    enable_pmultiqc          = true
    pmultiqc_idxml_skip      = true
    contaminant_string       = 'CONT'

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

    // Boilerplate options
    outdir                     = './results'
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    hook_url                   = System.getenv('HOOK_URL')
    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
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null

    // Schema validation default options
    validate_params            = true
}

// 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 profiles removed - Conda is no longer supported
    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'
        // see discussion: 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
        singularity.pullTimeout = '1 h'
        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'
    }
    // Micromamba profile removed - Conda is no longer supported
    // Aliases used by `nf-core pipelines download` (which calls
    // `nextflow inspect -profile singularity,test,test_full`) and by
    // anyone expecting the canonical nf-core profile names.
    test                { includeConfig 'conf/tests/test_dia.config'            }
    test_full           { includeConfig 'conf/tests/test_full_dia.config'       }
    test_dia            { includeConfig 'conf/tests/test_dia.config'            }
    test_dia_dotd       { includeConfig 'conf/tests/test_dia_dotd.config'       }
    test_dia_quantums   { includeConfig 'conf/tests/test_dia_quantums.config'   }
    test_dia_parquet    { includeConfig 'conf/tests/test_dia_parquet.config'     }
    test_dia_qpx        { includeConfig 'conf/tests/test_dia_qpx.config'         }
    test_dia_2_2_0      { includeConfig 'conf/tests/test_dia_2_2_0.config'     }
    test_latest_dia     { includeConfig 'conf/tests/test_latest_dia.config'     }
    test_full_dia       { includeConfig 'conf/tests/test_full_dia.config'       }
    test_dda            { includeConfig 'conf/tests/test_dda.config'           }
    test_dia_skip_preanalysis { includeConfig 'conf/tests/test_dia_skip_preanalysis.config' }
    // DIA-NN version overrides (used by merge_ci.yml matrix)
    diann_v1_8_1        { includeConfig 'conf/diann_versions/v1_8_1.config'    }
    diann_v2_1_0        { includeConfig 'conf/diann_versions/v2_1_0.config'    }
    diann_v2_2_0        { includeConfig 'conf/diann_versions/v2_2_0.config'    }
    diann_v2_3_2        { includeConfig 'conf/diann_versions/v2_3_2.config'    }
    diann_v2_5_0        { includeConfig 'conf/diann_versions/v2_5_0.config'    }
    dev             { includeConfig 'conf/dev.config'                   }
    pride_slurm     { includeConfig 'conf/pride_codon_slurm.config'     }
    manual_wave     { includeConfig 'conf/wave.config'                  }
    verbose_modules { includeConfig 'conf/modules/verbose_modules.config' }
    // mambaci         { includeConfig 'conf/mambaci.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 bigbio/quantmsdiann 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 pipeline-specific custom profiles (reuse quantms institutional configs)
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/quantms.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",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// 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            = 'bigbio/quantmsdiann'
    homePage        = 'https://github.com/bigbio/quantmsdiann'
    contributors    = [
        [
            name: 'Yasset Perez-Riverol',
            affiliation: 'European Bioinformatics Institute (EMBL-EBI), Cambridge, UK',
            email: 'ypriverol@gmail.com',
            github: 'ypriverol',
            contribution: ['maintainer', 'author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-6579-6941'
        ],
        [
            name: 'Dai Chengxin',
            affiliation: 'State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, Beijing, China',
            email: 'daichengxin999@gmail.com',
            github: 'daichengxin',
            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-6943-5211'
        ],
        [
            name: 'Julianus Pfeuffer',
            affiliation: 'Algorithmic Bioinformatics, Freie Universität Berlin, Berlin, Germany',
            email: 'jule.pf@gmail.com',
            github: 'jpfeuffer',
            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-8948-9209'
        ],
        [
            name: 'Dongze He',
            affiliation: 'Altos Labs, Inc.',
            email: 'dongzehe.zaza@gmail.com',
            github: 'DongzeHe',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-8259-7434'
        ],
        [
            name: 'Henry Webel',
            affiliation: 'DTU biosustain, Technical University of Denmark, Lyngby, Denmark',
            email: 'heweb@dtu.dk',
            github: 'enryh',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-8833-7617'
        ],
        [
            name: 'Fabian Egli',
            github: 'fabianegli',
            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: '0000-0001-5294-401X'
        ]
    ]
    description     = """DIA-NN quantitative mass spectrometry workflow built following nf-core guidelines"""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    nextflowVersion = '!>=25.10.4'
    version         = '2.1.0'
    doi             = '10.5281/zenodo.15573386'
}

// 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 per-workflow module configs for DSL2 module specific options
includeConfig 'conf/modules/shared.config'
includeConfig 'conf/modules/dia.config'