├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ └── release-announcments.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 ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-quantms_logo_light.png ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── check_samplesheet.py ├── diann_convert.py ├── msstats_plfq.R ├── msstats_tmt.R ├── msstats_utils.R ├── mzml_statistics.py └── prepare_diann_parameters.py ├── conf ├── base.config ├── big-nodes.config ├── dev.config ├── modules.config ├── test_dia.config ├── test_full_dia.config ├── test_full_lfq.config ├── test_full_tmt.config ├── test_lfq.config ├── test_lfq_sage.config ├── test_localize.config └── test_tmt.config ├── docs ├── README.md ├── images │ ├── full-DDA.svg │ ├── id-dda-pipeline.png │ ├── id_pipeline.png │ ├── id_pipeline.svg │ ├── mqc_fastqc_adapter.png │ ├── mqc_fastqc_counts.png │ ├── mqc_fastqc_quality.png │ ├── 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 ├── lib ├── NfcoreTemplate.groovy ├── Utils.groovy ├── WorkflowMain.groovy ├── WorkflowQuantms.groovy └── nfcore_external_java_deps.jar ├── main.nf ├── modules.json ├── modules ├── local │ ├── assemble_empirical_library │ │ ├── main.nf │ │ └── meta.yml │ ├── decompress_dotd │ │ ├── main.nf │ │ └── meta.yml │ ├── diann_preliminary_analysis │ │ ├── main.nf │ │ └── meta.yml │ ├── diannconvert │ │ ├── main.nf │ │ └── meta.yml │ ├── diannsummary │ │ ├── main.nf │ │ └── meta.yml │ ├── generate_diann_cfg │ │ ├── main.nf │ │ └── meta.yml │ ├── individual_final_analysis │ │ ├── main.nf │ │ └── meta.yml │ ├── msstats │ │ ├── main.nf │ │ └── meta.yml │ ├── msstatstmt │ │ ├── main.nf │ │ └── meta.yml │ ├── mzmlstatistics │ │ ├── main.nf │ │ └── meta.yml │ ├── openms │ │ ├── consensusid │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── decoydatabase │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── epifany │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── extractpsmfeatures │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── falsediscoveryrate │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── filemerge │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── idconflictresolver │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── idfilter │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── idmapper │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── idpep │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── idscoreswitcher │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── indexpeptides │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── isobaricanalyzer │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── msstatsconverter │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── mzmlindexing │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── openmspeakpicker │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── proteininference │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── proteinquantifier │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── proteomicslfq │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ └── thirdparty │ │ │ ├── luciphoradapter │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ │ ├── percolator │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ │ ├── searchenginecomet │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ │ ├── searchenginemsgf │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ │ └── searchenginesage │ │ │ ├── main.nf │ │ │ └── meta.yml │ ├── pmultiqc │ │ ├── main.nf │ │ └── meta.yml │ ├── preprocess_expdesign.nf │ ├── samplesheet_check.nf │ ├── sdrfparsing │ │ ├── main.nf │ │ └── meta.yml │ ├── silicolibrarygeneration │ │ ├── main.nf │ │ └── meta.yml │ ├── tdf2mzml │ │ ├── main.nf │ │ └── meta.yml │ └── thermorawfileparser │ │ ├── main.nf │ │ └── meta.yml └── nf-core │ ├── custom │ └── dumpsoftwareversions │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── dumpsoftwareversions.py │ └── multiqc │ ├── main.nf │ └── meta.yml ├── nextflow.config ├── nextflow_schema.json ├── pyproject.toml ├── subworkflows └── local │ ├── create_input_channel.nf │ ├── databasesearchengines.nf │ ├── featuremapper.nf │ ├── file_preparation.nf │ ├── id.nf │ ├── input_check.nf │ ├── phosphoscoring.nf │ ├── proteininference.nf │ ├── proteinquant.nf │ ├── psmfdrcontrol.nf │ └── psmrescoring.nf ├── tower.yml └── workflows ├── dia.nf ├── lfq.nf ├── quantms.nf └── tmt.nf /.devcontainer/devcontainer.json: 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