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Published June 17, 2024 | Version 2.6.0
Software Open

nf-core/mhcquant: MHCquant 2.6.0 - Mr Bob

Creators

  • 1. Peptide-based Immunotherapy
  • 2. @scverse @laminlabs @theislab
  • 3. Boehringer Ingelheim
  • 4. @seqeralabs
  • 5. German Human Genome-Phenome Archive
  • 6. QBiC @qbicsoftware
  • 7. Robert Bosch GmbH

Description

Added

  • Added MS²Rescore module with the underlying python CLI #293
  • Added support for handling various archive formats: d|d.tar.gz|d.tar|d.zip|mzML.gz|raw|RAW|mzML #323
  • Added test for timsTOF data #323
  • Added new flag --ms2pip_model_dir, which allows specifying a cache directory for ms2pip models #322

Fixed

  • Create only one decoy database #299
  • Template update 2.11 #300
  • Template update 2.12 #303
  • Use groupKey to streamline group-wise processing #310
  • Replace PYOPENMS_IDFILTER with OPENMS_IDFILTER #310
  • Added nf-core modules #310
  • Template update 2.13 #311
  • Template update 2.13.1 #313
  • Template update 2.14.1 #320
  • Added stubs to local modules #326

Changed

  • Set identification mode as default and rename --skip_quantification to --quantify #323

Deprecated

  • Removed MS²PIP and DeepLC modules. These feature generators are now called via the MS²Rescore framework #293. --use_deeplc and --use_ms2pip were aligned with MS²Rescore's feature generators and can be specified now with --feature_generators deeplc,ms2pip. --ms2pip_model_name was renamed to --ms2pip_model

Files

nf-core/mhcquant-2.6.0.zip

Files (2.7 MB)

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md5:83c44d6cd57da9da4fb8d0398e27d1b9
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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/mhcquant/tree/2.6.0 (URL)

Software

Repository URL
https://github.com/nf-core/mhcquant