nf-core/metaboigniter v2.0.1 - Purple Tulip

This latest version brings some minor updates and enhancements:

• Default change: Default negative adducts have been changed to H-1:-:0.8 H-3O-1:-:0.2
• Missing output data after peak picking have been resolved
• The issue with long file names in the alignment has been fixed
• Charge state handling in negative mode has been improved
• C13 detection is now only applied if the identification flag is set
• SIRIUS has been updated to 5.8.6
• MS2QUERY has been updated to 1.2.3
• New parameter ignore_msms_mapping_charge_pyopenms has been added to control the MS2 mapping if the charges are inconsistent between the consensus elements and the spectra

Thank you @axelwalter and @maxulysse for helping with this release.

nf-core/metaboigniter v2.0.0 - Purple Violet

This marks the release of Version 2.0.0 of our pipeline with the introduction of DSL 2 in nf-core/metaboigniter. This latest version brings an array of major updates and enhancements:

• Enhanced Input Handling: CSV file input format
• Quantification and Identification Features: We have added mapAlignerPoseClustering, featureLinkerUnlabeledkd, MetaboliteAdductDecharger, and MS2Query.
• Resolved Bugs: We've addressed and fixed issues related to SIRIUS APIs
• Performance: Parallel linking and identification

Deprecated Features:
We have deprecated several features from version 1.0.1. These include XCMS, IPO, MetFrag, CFMID, and Internal library search.

A huge thanks to @axelwalter and @maxulysse for helping with this release.

nf-core/metaboigniter v1.0.1 - Red Daisy

Minor patch release that includes:

• Fixed running the pipeline on AWS.
• Unused parameters were removed
• Template has been updated to nf-core/tools v1.14

nf-core/metaboigniter v1.0.0 - Teal Rose

The initial release of nf-core/metaboigniter pipeline.

This release includes:

• IPO parameter tuning
• mass trace detection using XCMS or OpenMS
• Retention time alignment and grouping
• Adduct and isotope detection
• Noise filtering using QC stability, blank filtering, and dilution series
• Metabolite identification using FINGER:ID, MetFrag, CFM-ID, and Internal library
• Normalization and transformation