├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── branch.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── diann_private.yml │ ├── extended_ci.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ └── template-version-comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── itraq4plex_default_correction.matrix ├── itraq8plex_default_correction.matrix ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-quantms_logo_light.png ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json ├── tmt11plex_default_correction.matrix ├── tmt6plex_90064_XL352952_correction.matrix ├── tmt6plex_default_correction.matrix └── tmt6plex_msnbase_correction.matrix ├── bin ├── msstats_plfq.R ├── msstats_tmt.R └── msstats_utils.R ├── conf ├── base.config ├── dev.config ├── modules │ ├── modules.config │ └── verbose_modules.config ├── pride_codon_slurm.config ├── tests │ ├── test_dda_id.config │ ├── test_dia.config │ ├── test_full_dia.config │ ├── test_full_lfq.config │ ├── test_full_tmt.config │ ├── test_latest_dia.config │ ├── test_lfq.config │ ├── test_lfq_sage.config │ ├── test_localize.config │ ├── test_tmt.config │ └── test_tmt_corr.config └── wave.config ├── docs ├── README.md ├── images │ ├── full-DDA.svg │ ├── id-dda-pipeline.png │ ├── id_pipeline.png │ ├── id_pipeline.svg │ ├── ms-proteomics.png │ ├── msms.png │ ├── nf-core-quantms_logo_dark.png │ ├── nf-core-quantms_logo_light.png │ ├── quantms.png │ ├── quantms.svg │ ├── quantms_lfq.svg │ ├── quantms_metro.drawio.svg │ └── quantms_metro.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── diann │ │ ├── assemble_empirical_library │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── convert_results │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── final_quantification │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── generate_cfg │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── individual_analysis │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── insilico_library_generation │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ └── preliminary_analysis │ │ │ ├── main.nf │ │ │ └── meta.yml │ ├── msstats │ │ ├── msstats_lfq │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ └── msstats_tmt │ │ │ ├── main.nf │ │ │ └── meta.yml │ ├── openms │ │ ├── comet │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── consensusid │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── false_discovery_rate │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── file_merge │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── generate_decoy_database │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── id_conflict_resolver │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── id_filter │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── id_mapper │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── id_merger │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── id_ripper │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── id_score_switcher │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── index_peptides │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── isobaric_analyzer │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── luciphor │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── msgf │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── msstats_converter │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── mzml_indexing │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── openms_peak_picker │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── percolator │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── protein_inference_epifany │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── protein_inference_generic │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── protein_quantifier │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── proteomicslfq │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ └── sage │ │ │ ├── main.nf │ │ │ └── meta.yml │ ├── pmultiqc │ │ ├── main.nf │ │ └── meta.yml │ ├── preprocess_expdesign │ │ ├── main.nf │ │ └── meta.yml │ ├── samplesheet_check │ │ ├── main.nf │ │ └── meta.yml │ ├── sdrf_parsing │ │ ├── main.nf │ │ └── meta.yml │ ├── thermorawfileparser │ │ ├── main.nf │ │ └── meta.yml │ └── utils │ │ ├── decompress_dotd │ │ ├── main.nf │ │ └── meta.yml │ │ ├── extract_sample │ │ ├── main.nf │ │ └── meta.yml │ │ ├── msgf_db_indexing │ │ ├── main.nf │ │ └── meta.yml │ │ ├── msrescore_features │ │ ├── main.nf │ │ └── meta.yml │ │ ├── mzml_statistics │ │ ├── main.nf │ │ └── meta.yml │ │ ├── psm_clean │ │ ├── main.nf │ │ └── meta.yml │ │ ├── psm_conversion │ │ ├── main.nf │ │ └── meta.yml │ │ ├── spectrum_features │ │ ├── main.nf │ │ └── meta.yml │ │ └── tdf2mzml │ │ ├── main.nf │ │ └── meta.yml └── nf-core │ └── custom │ └── dumpsoftwareversions │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── templates │ └── dumpsoftwareversions.py │ └── tests │ ├── main.nf.test │ └── main.nf.test.snap ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── create_input_channel │ │ ├── main.nf │ │ └── meta.yml │ ├── dda_id │ │ ├── main.nf │ │ └── meta.yml │ ├── feature_mapper │ │ ├── main.nf │ │ └── meta.yml │ ├── file_preparation │ │ ├── main.nf │ │ └── meta.yml │ ├── id │ │ ├── main.nf │ │ └── meta.yml │ ├── input_check │ │ ├── main.nf │ │ └── meta.yml │ ├── peptide_database_search │ │ ├── main.nf │ │ └── meta.yml │ ├── phospho_scoring │ │ ├── main.nf │ │ └── meta.yml │ ├── protein_inference │ │ ├── main.nf │ │ └── meta.yml │ ├── protein_quant │ │ ├── main.nf │ │ └── meta.yml │ ├── psm_fdr_control │ │ ├── main.nf │ │ └── meta.yml │ ├── psm_rescoring │ │ ├── main.nf │ │ └── meta.yml │ └── utils_nfcore_quantms_pipeline │ 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