nf-core/mhcquant: 3.3.0 - Favorite

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 |