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@jonasscheid jonasscheid released this 02 Oct 13:43
3.3.0
a4b6d51
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Added

  • Added MultiQC plot for DeepLC retention time calibration per sample #461
  • Added MultiQC box plot of aligned residuals in the quant workflow #462
  • Added manifest.diagram to nextflow.config by @ewels #476

Fixed

  • Fixed UNTAR, UNZIP and EPICORE version eval crashing on parenthesis-containing tool banners #455
  • Fixed silent per-sample drop from order-dependent combine(by:) in QUANT #460
  • Fixed non-reproducible per-replicate column order in quantification output from unsorted groupTuple() #460
  • Restored documented samplesheet validation errors for malformed input #463
  • Fixed Condition samplesheet validation accepting values with whitespace #464
  • Fixed FeatureFinderIdentification (OpenMS 3.5.0) losing all peptide identifications on FAIMS data, which crashed SUMMARIZE_RESULTS, by disabling faims:merge_features #474
  • Fixed MapAlignerIdentification aborting with no data points for 'linear' model when a run shares no RT landmarks with its group; the whole sample/condition group is now excluded from quantification, exported with identifications only, and a warning is emitted #474
  • Fixed test_single_quant nf-test never running the QUANT subworkflow #475
  • Fixed missing ion mobility for timsTOF .d input by bumping tdf2mzml to 0.6.1 #479

Changed

  • Updated to nf-core template 4.0.2 #454
  • Updated to nf-core template 4.0.3 #468
  • Updated to nf-core template 4.1.0 #472
  • Updated all nf-core modules to their latest versions #454
  • Replaced local pridepy/download_file with upstream nf-core pridepy/downloadfile #457
  • Bumped nf-schema plugin to 2.7.2 #465
  • Stopped publishing the intermediate _psm.idXML and _ms2rescore.idXML files to intermediate_results/rescoring #470
  • Replaced local easypqp/convert and easypqp/library modules with the nf-core/modules equivalents #473
  • Replaced local OpenMS modules (MzTabExporter, MapAlignerIdentification, MapRTTransformer, FeatureFinderIdentification, IDConflictResolver, PSMFeatureExtractor) with the nf-core/modules equivalents #477
  • Updated utils_nfcore_pipeline subworkflow and easypqp/convert module to their latest versions and added missing tool citations #480
  • Changed MultiQC box plot whiskers from min/max to 1.5 × IQR #482

Dependencies

Dependency Old version New version
easypqp 0.1.57 0.1.59
MultiQC 1.33.0 1.35.0
Nf-core 3.5.1 4.1.0
tdf2mzml 0.5.0 0.6.1

Contributors

ewels
Assets 2
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