Version history

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.

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.

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

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
    , MetFrag, CFM-ID, and Internal library
  • Normalization and transformation