nextflow.config

params {

    config_profile_name= 'Metabolomics Datatype Course'
    config_profile_description = 'MONA and DSP metabolomics data processing training'

    outdir = 'results'

    config_profile_name        = 'Metabonaut example dataset'
    config_profile_description = 'Example data from Metabonaut.'

    // Limit resources so that this can run on GitHub Actions
    max_cpus   = 4
    max_memory = '8.GB'
    max_time   = '6.h'

    // Input data
    input  = 'data/MTBLS8735/samplesheet.csv'
    // Only one charge
    // algorithm_ffm_charge_upper_bound_featurefindermetabo_openms=1

    // identification related

    // identification = true
    // run_ms2query = true
    // run_sirius = true


    // Default peakpickerhires_openms
    algorithm_signal_to_noise_peakpickerhires_openms = 0.1
    algorithm_spacing_difference_gap_peakpickerhires_openms = 4.0
    // algorithm_spacing_difference_peakpickerhires_openms = 1.5
    // algorithm_missing_peakpickerhires_openms = 1
    // algorithm_report_fwhm_peakpickerhires_openms = false
    // algorithm_report_fwhm_unit_peakpickerhires_openms = "relative"
    // algorithm_signaltonoise_max_intensity_peakpickerhires_openms = -1
    algorithm_signaltonoise_auto_max_stdev_factor_peakpickerhires_openms = 3.0
    // algorithm_signaltonoise_auto_max_percentile_peakpickerhires_openms = 95
    // algorithm_signaltonoise_auto_mode_peakpickerhires_openms = 0
    // algorithm_signaltonoise_win_len_peakpickerhires_openms = 200.0
    // algorithm_signaltonoise_bin_count_peakpickerhires_openms = 30
    // algorithm_signaltonoise_min_required_elements_peakpickerhires_openms = 10
    // algorithm_signaltonoise_noise_for_empty_window_peakpickerhires_openms = 1.0e20

    // Default featurefindermetabo_openms
    algorithm_common_noise_threshold_int_featurefindermetabo_openms = 60.0
    algorithm_common_chrom_peak_snr_featurefindermetabo_openms = 3.0
    // algorithm_common_chrom_fwhm_featurefindermetabo_openms = 5.0
    // algorithm_mtd_mass_error_ppm_featurefindermetabo_openms = 10.0
    // algorithm_mtd_reestimate_mt_sd_featurefindermetabo_openms = true
    // algorithm_mtd_quant_method_featurefindermetabo_openms = "area"
    // algorithm_mtd_trace_termination_criterion_featurefindermetabo_openms = "outlier"
    // algorithm_mtd_trace_termination_outliers_featurefindermetabo_openms = 5
    // algorithm_mtd_min_sample_rate_featurefindermetabo_openms = 0.5
    // algorithm_mtd_min_trace_length_featurefindermetabo_openms = 5.0
    // algorithm_mtd_max_trace_length_featurefindermetabo_openms = -1.0
    // algorithm_epd_enabled_featurefindermetabo_openms = true
    // algorithm_epd_width_filtering_featurefindermetabo_openms = "fixed"
    // algorithm_epd_min_fwhm_featurefindermetabo_openms = 1.0
    // algorithm_epd_max_fwhm_featurefindermetabo_openms = 60.0
    algorithm_epd_masstrace_snr_filtering_featurefindermetabo_openms = true // default: false
    // algorithm_ffm_local_rt_range_featurefindermetabo_openms = 10.0
    // algorithm_ffm_local_mz_range_featurefindermetabo_openms = 6.5
    // algorithm_ffm_charge_lower_bound_featurefindermetabo_openms = 1
    algorithm_ffm_charge_upper_bound_featurefindermetabo_openms = 1
    // algorithm_ffm_report_summed_ints_featurefindermetabo_openms = false
    // algorithm_ffm_enable_rt_filtering_featurefindermetabo_openms = true
    // algorithm_ffm_isotope_filtering_model_featurefindermetabo_openms = "metabolites (5% RMS)"
    // algorithm_ffm_mz_scoring_13c_featurefindermetabo_openms = false
    // algorithm_ffm_use_smoothed_intensities_featurefindermetabo_openms = true
    // algorithm_ffm_report_convex_hulls_featurefindermetabo_openms = false
    // algorithm_ffm_remove_single_traces_featurefindermetabo_openms = false
    // algorithm_ffm_mz_scoring_by_elements_featurefindermetabo_openms = false
    // algorithm_ffm_elements_featurefindermetabo_openms = "CHNOPS"

    // Default mapalignerposeclustering_openms
    algorithm_max_num_peaks_considered_mapalignerposeclustering_openms = 2000 // default: 1000
    // algorithm_superimposer_mz_pair_max_distance_mapalignerposeclustering_openms = 0.2
    // algorithm_superimposer_rt_pair_distance_fraction_mapalignerposeclustering_openms = 0.4
    // algorithm_superimposer_num_used_points_mapalignerposeclustering_openms = 2000
    // algorithm_superimposer_scaling_bucket_size_mapalignerposeclustering_openms = 5.0e-03
    // algorithm_superimposer_shift_bucket_size_mapalignerposeclustering_openms = 3.0
    // algorithm_superimposer_max_shift_mapalignerposeclustering_openms = 1000.0
    // algorithm_superimposer_max_scaling_mapalignerposeclustering_openms = 2.0
    // algorithm_superimposer_dump_buckets_mapalignerposeclustering_openms = ""
    // algorithm_superimposer_dump_pairs_mapalignerposeclustering_openms = ""
    // algorithm_pairfinder_second_nearest_gap_mapalignerposeclustering_openms = 2.0
    // algorithm_pairfinder_use_identifications_mapalignerposeclustering_openms = false
    // algorithm_pairfinder_ignore_charge_mapalignerposeclustering_openms = false
    // algorithm_pairfinder_ignore_adduct_mapalignerposeclustering_openms = true
    algorithm_pairfinder_distance_rt_max_difference_mapalignerposeclustering_openms = 45 // default: 65
    // algorithm_pairfinder_distance_rt_exponent_mapalignerposeclustering_openms = 1.0
    // algorithm_pairfinder_distance_rt_weight_mapalignerposeclustering_openms = 1.0
    // algorithm_pairfinder_distance_mz_max_difference_mapalignerposeclustering_openms = 15.0
    // algorithm_pairfinder_distance_mz_unit_mapalignerposeclustering_openms = "ppm"
    // algorithm_pairfinder_distance_mz_exponent_mapalignerposeclustering_openms = 2.0
    // algorithm_pairfinder_distance_mz_weight_mapalignerposeclustering_openms = 1.0
    // algorithm_pairfinder_distance_intensity_exponent_mapalignerposeclustering_openms = 1.0
    // algorithm_pairfinder_distance_intensity_weight_mapalignerposeclustering_openms = 0.0
    // algorithm_pairfinder_distance_intensity_log_transform_mapalignerposeclustering_openms = "disabled"

    // Default maprttransformer_openms
    // invert_maprttransformer_openms = false
    // store_original_rt_maprttransformer_openms = false
    // model_type_maprttransformer_openms = "none"
    // model_linear_symmetric_regression_maprttransformer_openms = false
    // model_linear_x_weight_maprttransformer_openms = "x"
    // model_linear_y_weight_maprttransformer_openms = "y"
    // model_linear_x_datum_min_maprttransformer_openms = 1.0e-15
    // model_linear_x_datum_max_maprttransformer_openms = 1.0e15
    // model_linear_y_datum_min_maprttransformer_openms = 1.0e-15
    // model_linear_y_datum_max_maprttransformer_openms = 1.0e15
    // model_b_spline_wavelength_maprttransformer_openms = 0.0
    // model_b_spline_num_nodes_maprttransformer_openms = 5
    // model_b_spline_extrapolate_maprttransformer_openms = "linear"
    // model_b_spline_boundary_condition_maprttransformer_openms = 2
    // model_lowess_span_maprttransformer_openms = 0.666666666666667
    // model_lowess_num_iterations_maprttransformer_openms = 3
    // model_lowess_delta_maprttransformer_openms = -1.0
    // model_lowess_interpolation_type_maprttransformer_openms = "cspline"
    // model_lowess_extrapolation_type_maprttransformer_openms = "four-point-linear"
    // model_interpolated_interpolation_type_maprttransformer_openms = "cspline"
    // model_interpolated_extrapolation_type_maprttransformer_openms = "two-point-linear"


    // Default featurelinkerunlabeledkd_openms
    // keep_subelements_featurelinkerunlabeledkd_openms = false
    // algorithm_mz_unit_featurelinkerunlabeledkd_openms = "ppm"
    // algorithm_nr_partitions_featurelinkerunlabeledkd_openms = 100
    // algorithm_warp_enabled_featurelinkerunlabeledkd_openms = true
    algorithm_warp_rt_tol_featurelinkerunlabeledkd_openms = 45.0 // default: 100.0
    algorithm_warp_mz_tol_featurelinkerunlabeledkd_openms = 3.0 // default: 4
    // algorithm_warp_max_pairwise_log_fc_featurelinkerunlabeledkd_openms = 0.5
    // algorithm_warp_min_rel_cc_size_featurelinkerunlabeledkd_openms = 0.5
    // algorithm_warp_max_nr_conflicts_featurelinkerunlabeledkd_openms = 0
    algorithm_link_rt_tol_featurelinkerunlabeledkd_openms = 12.0 // default: 30.0
    algorithm_link_mz_tol_featurelinkerunlabeledkd_openms = 6.0 // default: 10.0
    // algorithm_link_charge_merging_featurelinkerunlabeledkd_openms = "With_charge_zero"
    // algorithm_link_adduct_merging_featurelinkerunlabeledkd_openms = "Any"
    // algorithm_distance_rt_exponent_featurelinkerunlabeledkd_openms = 1.0
    // algorithm_distance_rt_weight_featurelinkerunlabeledkd_openms = 1.0
    // algorithm_distance_mz_exponent_featurelinkerunlabeledkd_openms = 2.0
    // algorithm_distance_mz_weight_featurelinkerunlabeledkd_openms = 1.0
    // algorithm_distance_intensity_exponent_featurelinkerunlabeledkd_openms = 1.0
    // algorithm_distance_intensity_weight_featurelinkerunlabeledkd_openms = 1.0
    // algorithm_distance_intensity_log_transform_featurelinkerunlabeledkd_openms = "enabled"
    // algorithm_lowess_span_featurelinkerunlabeledkd_openms = 0.666666666666667
    // algorithm_lowess_num_iterations_featurelinkerunlabeledkd_openms = 3
    // algorithm_lowess_delta_featurelinkerunlabeledkd_openms = -1.0
    // algorithm_lowess_interpolation_type_featurelinkerunlabeledkd_openms = "cspline"
    // algorithm_lowess_extrapolation_type_featurelinkerunlabeledkd_openms = "four-point-linear"


    // Default metaboliteadductdecharger_openms
    // algorithm_metabolitefeaturedeconvolution_charge_min_metaboliteadductdecharger_openms = 1
    // algorithm_metabolitefeaturedeconvolution_charge_max_metaboliteadductdecharger_openms = 1
    // algorithm_metabolitefeaturedeconvolution_charge_span_max_metaboliteadductdecharger_openms = 1
    // algorithm_metabolitefeaturedeconvolution_q_try_metaboliteadductdecharger_openms = "feature"
    // algorithm_metabolitefeaturedeconvolution_retention_max_diff_metaboliteadductdecharger_openms = 1.0
    // algorithm_metabolitefeaturedeconvolution_retention_max_diff_local_metaboliteadductdecharger_openms = 1.0
    // algorithm_metabolitefeaturedeconvolution_mass_max_diff_metaboliteadductdecharger_openms = 5
    // algorithm_metabolitefeaturedeconvolution_unit_metaboliteadductdecharger_openms = "ppm"
    // algorithm_metabolitefeaturedeconvolution_max_neutrals_metaboliteadductdecharger_openms = 1
    // algorithm_metabolitefeaturedeconvolution_use_minority_bound_metaboliteadductdecharger_openms = true
    // algorithm_metabolitefeaturedeconvolution_max_minority_bound_metaboliteadductdecharger_openms = 1
    // algorithm_metabolitefeaturedeconvolution_min_rt_overlap_metaboliteadductdecharger_openms = 0.66
    // algorithm_metabolitefeaturedeconvolution_intensity_filter_metaboliteadductdecharger_openms = false
    // algorithm_metabolitefeaturedeconvolution_default_map_label_metaboliteadductdecharger_openms = "decharged features"





    // Defaults for featurefindermetaboident_openms
        // extract_mz_window_featurefindermetaboident_openms = 10.0
        // extract_rt_window_featurefindermetaboident_openms = 0.0
        // extract_n_isotopes_featurefindermetaboident_openms = 2
        // extract_isotope_pmin_featurefindermetaboident_openms = 0.0
        // detect_peak_width_featurefindermetaboident_openms = 60.0
        // detect_min_peak_width_featurefindermetaboident_openms = 0.2
    detect_signal_to_noise_featurefindermetaboident_openms = 1.0 // 0.8
    // model_type_featurefindermetaboident_openms = "symmetric"
    // model_add_zeros_featurefindermetaboident_openms = 0.2
    // model_unweighted_fit_featurefindermetaboident_openms = false
    // model_no_imputation_featurefindermetaboident_openms = true
    // model_each_trace_featurefindermetaboident_openms = false
    // model_check_min_area_featurefindermetaboident_openms = 1.0
    // model_check_boundaries_featurefindermetaboident_openms = 0.5
    // model_check_width_featurefindermetaboident_openms = 10.0
    // model_check_asymmetry_featurefindermetaboident_openms = 10.0
    // emgscoring_max_iteration_featurefindermetaboident_openms = 100
    // emgscoring_init_mom_featurefindermetaboident_openms = false


    // Defaults for splitmgf_pyopenms
    // mgf_splitmgf_pyopenms=1


    // General params
    // skip_centroiding=true
    // polarity="positive"
    // ms2_collection_model="paired" // separate means the MS2 files are different than MS1. Anything else will be treated as having MS1 and 2 in a single file
    // requantification=false
    // identification=false
    // skip_alignment=false
    // skip_adduct_detection=false
    // adducts_pos="H:+:0.6 Na:+:0.1 NH4:+:0.1 H-1O-1:+:0.1 H-3O-2:+:0.1"
    // adducts_neg="H-1:-:0.8 H-3O-1:-:0.2"
    // parallel_linking = false

    // ms2 query
    // run_ms2query = false
    // offline_model_ms2query=false
    // models_dir_ms2query="models"
    // train_library_ms2query=false
    // library_path_ms2query=""

    // MSmapping Params
    // mz_tolerance_pyopenms=20.0
    // rt_tolerance_pyopenms = 5.0
    // annotate_ids_with_subelements_pyopenms = true
    // measure_from_subelements_pyopenms = true
    // ignore_msms_mapping_charge_pyopenms = false

    // ms2_processing
    // ms2_use_feature_ionization = false
    // ms2_feature_selection = "quality" // possible values: intensity quality
    // ms2_normalized_intensity = true
    // ms2_iterations = 3
    // ms2_ppm_map = 10

}