MHCquant 3.0.0 - Monrepos

Added

• Added PYOPENMS_CHROMATOGRAMEXTRACTOR extracting MS1 Chromatograms and visualize them in multiQC report #329
• Added OPENMS_IDMASSACCURACY and DATAMASH_HISTOGRAM to compute fragment mass errors and visualizte them in multiQC report #332
• Added global fdr evaluation in new local subworkflow RESCORE #338
• Added -weights parameter in OPENMS_PERCOLATORADAPTER and visualize the median feature weights in multiQC report #347
• Added flag --generate_speclib that will generate a spectrum library for DIA searches with EasyPQP #349
• Replace local with nf-core modules #350
• Added support for CCS-based rescoring with IM2Deep feature generator #358
• Added multiple plots to MultiQC report by @JuliaGraf #361
• Added ability to reduce output columns by @JuliaGraf #361 (BREAKING)

Dependencies

Dependency	Old version	New version
MultiQC	1.21.0	1.28.0
MS2Rescore	3.0.1	3.1.5
Nf-core	2.14.1	3.2.1
OpenMS	3.1.0	3.4.0
Thermorawfileparser	1.4.3	1.4.5

MHCquant 2.6.0 - Mr Bob

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

mhcquant 2.5.0 - Angry Bird

Added

• #267 Support for brukers tdf format by adding tdf2mzml converter
• #269 DeepLC retention time prediction (shout out to @steffenlem)
• #270 MS2PIP peak intensity prediction (shout out to @steffenlem)
• #271 Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0 (optional)
• Made file extension check case insensitive
• Added option to provide a default comet parameters file @steffenlem
• #273 Optimize resource allocations
• #274 Template update 2.9
• #280 Improved quantification such that merged FDR-filtered runs can be quantified properly
• #282 Template update 2.10

Fixed

• #266 New OpenMS version 3.0.0 fixes duplicated ID bug #250

Dependencies

• #266 Switched from OpenMS version 2.8.0 to newest version 3.0.0
• #266 Bumped ThermoRawFileParser version from 1.4.0 to 1.4.2

Deprecated

• #280 OpenMS RT prediction

mhcquant 2.4.1 - Young Shark

Added

• Added low resolution settings (e.g. Iontrap) #254 @steffenlem

Fixed

• Increased comet search, through altering the spectrum_batch_size from 500 to 0
• #249 - nf-core template update (version 2.7.2) @marissaDubbelaar
• #258 - Adjusted decoy strategy to reverse #255 and made consistent fdr-level flags #228
• #845 - Adjusted nf-core test data set #233

mhcquant 2.4.0 - Maroon Gold Boxer

Added

• Additional output from CometAdapter (generated with the parameter --pin_out)
• Folder structure within the intermediate_results folder to retrace the outcome files easier
• OPENMS_FALSEDISCOVERYRATE and OPENMS_IDFILTER_FOR_ALIGNMENT are now included in the first quantification step
• Altered the outcome content with the inclusion of the different folder structure
• Updated the mhcquant_web.png in the assets folder
• #229 Add ion annotation feature requested in #220
• #235 Add the annotate_ions parameter to enable/disable the ion annotation feature (default is false)

Fixed

• Resolved issues with SAMPLESHEET_CHECK
• Fix for the peakpickerhires, mzml files generated from input raw files are now seen as input for this step as well
• PRE_QUANTIFICATION is renamed to MAP_ALIGNMENT to indicate that the alignment (and the complementing processes) of the different maps happens here
• POST_QUANTIFICATION is renamed to PROCESS_FEATURE since the feature identification and processing is done here
• Outcome of OPENMS_FEATUREFINDERIDENTIFICATION got lost during one of the previous updates, this is reintroduced
• OPENMS_TEXTEXPORTER_UNQUANTIFIED and OPENMS_TEXTEXPORTER_QUANTIFIED return only significant hits again
• #226 - nf-core template update (version 2.6)
• #230 - Issue with OPENMS_MZTABEXPORTER_QUANT
• #236 - Resolved issue with PYOPENMS_IONANNOTATOR
• Fix for an inconsistent mzml channel issue
• #241 - Fix of the HLA allele annotation in the help of the allele_sheet parameter

Dependencies

• Updated the multiQC module

Dependency	Old version	New version
MultiQC	1.11	1.12
OpenMS	2.6.0	2.8.0
OpenMS thirdparty	2.6.0	2.8.0
pyOpenMS	-	2.8
thermorawfileparser	1.3.4	1.4.0

Deprecated

• OPENMS_TEXTEXPORTER_PSMS was removed due to the outcome of the comet adapter step

nfcore/mhcquant v2.3.1 - White Gold Swallow

Added

• #210 - Icons to the different parameters in the nextflow_schema.json

Fixed

• #211 Resolved the problem that there was no output from OPENMS_MZTABEXPORTER_QUANT
• #212 - Altered the CometAdapter functionalities for resolve the issue with the fixed_mods

nfcore/mhcquant v2.3.0 - White Gold Swallow

Added

• #206 Updated the workflow picture
• Adjustments of the PRE_QUANTIFICATION subworkflow: OPENMS_FALSEDISCOVERYRATE, OPENMS_IDFILTER_FOR_ALIGNMENT, and OPENMS_TEXTEXPORTER_PSMS
• Included OPENMS_TEXTEXPORTER_UNQUANTIFIEDto write a combined FDR filtered output file for unquantified data
• Included pipeline summary and increment the documentation paragraph
• #195 Updated parameter documentation
• #189 Added backslashes in Quick Start in README
• #188 Added reference links to README

Fixed

• Typo in previous release date
• #208 - nf-core template update (version 2.3.2)
• #199 Fixes some typos and stuff in the output documentation
• #192 Fixed samplesheet format in usage.md
• #184 Fix parsing for VEP annotated VCF files

Dependencies

Dependency	Old version	New version
MultiQC	1.11	1.12

Deprecated

• #191 Removed the table of contents from usage.md

nf-core/mhcquant v2.2.0 - Silver Titanium Ostrich

Added

• Included the newest nf-core template (version 2.2)
• Adjustment of the README, including all contributors
• Inclusion of the PSMs files (tsv format) per replicates in results/PSMs
• Include check-in WorkflowMhcquant, to determine if the allele and vcf sheet has been provided under specific circumstances

Fixed

• Changed parameters in the nextflow_schema.json to be in coherence with the nextflow.config
• Error that was raised in generate_proteins_from_vcf
• Problems that were detected in predict_possible_class1_neoepitopes and predict_possible_class2_neoepitopes
• Error that occurred in mhcnuggets_predictneoepitopesclass2 (faulty container set up)

Dependencies

Dependency	Old version	New version
fred2	2.0.6	2.0.7

nf-core/mhcquant v2.1.0 -Olive Tin Hamster

Added

• Inclusion of assets/schema_input.json
• Added the MultiQC again to report the versions
• MHCquant parameters are now directly assigned to the argument of the process

Fixed

• Fixed typos
• Change the version annotation
• Renaming of various processes (functionality remained the same)
• #165 - Raise memory requirements of FeatureFinderIdentification step
• #176 - Pipeline crashes when setting the --skip_quantification flag

Dependencies

Dependency	Old version	New version
openms	2.5.0	2.6.0
openms-thirdparty	2.5.0	2.6.0
thermorawfileparser	1.2.3	1.3.4

nf-core/mhcquant v2.0.0 - Steel Beagle

Enhancements

• DSL1 to DSL2 conversion
• Different processes based on a unique step in the pipeline
• Inclusion of one sub-workflow: refine FDR on a predicted subset
• The process: openms_cometadapter includes commented lines (which could be used as a reference for future module development)
• MHCquant pipeline runs from workflows/mhcquant.nf instead of the main
• Template update to nf-core/tools 2.1