├── .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 │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ └── release-announcements.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core-lint.yaml ├── .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 ├── emptyfile.idXML ├── m2query_model_negative.csv ├── m2query_model_positive.csv ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-metaboigniter_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── analog_annotation.py ├── c13detection.py ├── calc_feature_boundries.py ├── check_samplesheet.py ├── checkfiles_ms2query.py ├── clean_ms2_cons.py ├── cleanup.py ├── conc_tsv.py ├── download_model.py ├── download_models.sh ├── extract_feature_mz.py ├── extract_mapping.py ├── file_merger_consensus.py ├── fulltrain_ms2query.py ├── generate_ms_params.py ├── ismapping.py ├── lib_generator.py ├── merge.py ├── reloadmaps.py ├── sirius_params_single.py ├── siriussearch.sh ├── split.py ├── split_consensus.py ├── split_features.py ├── split_mgf.py └── train_ms2query.py ├── conf ├── base.config ├── modules.config ├── test.config └── test_full.config ├── docs ├── README.md ├── images │ ├── MetaboIgniter-Metro-Map.svg │ ├── Metaboigniter_graph.png │ ├── metaboigniter_metro_map.png │ ├── nf-core-metaboigniter_logo_dark.png │ └── nf-core-metaboigniter_logo_light.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── general_mergefile.nf │ ├── ms2query_checkmodelfiles.nf │ ├── ms2query_downloadmodel.nf │ ├── ms2query_export.nf │ ├── ms2query_modelfulltrain.nf │ ├── ms2query_modeltrain.nf │ ├── ms2query_search.nf │ ├── openms_featurefindermetabo.nf │ ├── openms_featurefindermetaboident.nf │ ├── openms_featurelinkerunlabeledkd.nf │ ├── openms_filefilter.nf │ ├── openms_gnpsexport.nf │ ├── openms_idmapper.nf │ ├── openms_idmapperconsensus.nf │ ├── openms_mapalignerposeclustering.nf │ ├── openms_mapalignerposeclusteringmzml.nf │ ├── openms_maprttransformer.nf │ ├── openms_metaboliteadductdecharger.nf │ ├── openms_peakpickerhires.nf │ ├── openms_siriusparams.nf │ ├── pyopenms_c13detection.nf │ ├── pyopenms_calculateboundries.nf │ ├── pyopenms_conctsv.nf │ ├── pyopenms_export.nf │ ├── pyopenms_extractfeaturemz.nf │ ├── pyopenms_extractmapping.nf │ ├── pyopenms_filemerger.nf │ ├── pyopenms_generatesearchparams │ ├── pyopenms_generatesearchparams.nf │ ├── pyopenms_generatesearchparamsunmapped.nf │ ├── pyopenms_isomapping.nf │ ├── pyopenms_libbuilder.nf │ ├── pyopenms_merge.nf │ ├── pyopenms_msmapping.nf │ ├── pyopenms_reloadmaps.nf │ ├── pyopenms_removedup.nf │ ├── pyopenms_split.nf │ ├── pyopenms_splitconsensus.nf │ ├── pyopenms_splitfeaturexml.nf │ ├── pyopenms_splitmgf.nf │ └── sirius_search.nf └── nf-core │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ └── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── pyproject.toml ├── subworkflows ├── local │ ├── annotation.nf │ ├── identification.nf │ ├── linker.nf │ ├── ms2query.nf │ ├── ms2query_modeldownloader.nf │ ├── quantification.nf │ ├── requantification.nf │ ├── sirius.nf │ └── utils_nfcore_metaboigniter_pipeline │ │ └── main.nf └── nf-core │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ 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