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

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
• https://github.com/nf-core/mhcquant/pull/274 Template update 2.9
• #280 Improved quantification such that merged FDR-filtered runs can be quantified properly
• https://github.com/nf-core/mhcquant/pull/282 Template update 2.10

Fixed

• https://github.com/nf-core/mhcquant/pull/266 New OpenMS version 3.0.0 fixes duplicated ID bug https://github.com/nf-core/mhcquant/issues/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

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

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

Deprecated

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

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

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

Deprecated

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

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

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

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

Added

• Template update to 1.10.2
• Added parameter json schema
• Added full size AWS test profile
• Included new parameters for Neutral loss and precursor ion inclusion

Fixed

• Changed trigger for AWS tests

Bugfix release:

• optimal cluster configuration
• fixed duplication of ids/mixing of channels

• raise OpenMS version to 2.5
• adapt workflow accordingly with new options
• integrate sample, allele and vcf sheets instead of file dirs
• remove specifying input as file directorys eg. “data/*.mzML”
• branched mzML/raw input
• introduce param to skip quantification

Template Update Raw File Reading Quantification FDR Retention Time Prediction MHCFlurry, MHCNugget, Percolator version increase

v1.2.6 nf-core/mhcquant “Golden Eagle” - 2019/03/05

Fixed

linear retention time alignment refine_fdr README

v1.2.5 nf-core/mhcquant “Golden Eagle” - 2019/03/04

Fixed

sort channels by basename fixed psm-level-fdrs

v1.2.4 nf-core/mhcquant “Golden Eagle” - 2019/02/06 Fixed fixed refine_fdr_on_predicted_subset float error

v1.2.3 nf-core/mhcquant “Golden Eagle” - 2019/02/02

Fixed filter out uncommon aminoacids U,X,B,J,Z

v1.2.2 nf-core/mhcquant “Golden Eagle” - 2019/01/28

Fixed

default params to false change on centroidisation parameter small changes on docu

v1.2.1 nf-core/mhcquant “Golden Eagle” - 2019/01/24

Fixed

process identical names bug

v1.2.0 nf-core/mhcquant “Golden Eagle” - 2019/01/19

Added

• Subset FDR refinement option
• Fred2 dependency
• vcf parser and translation to proteins

Updates since 1.0.0:

• mhcflurry conda package added
• mhcflurry predictions added
• peak picking preprocessing added
• minor changes in default parameters
• few arguments added eg. min_peptide_len, max_peptide_len

This is the initial pipeline release of nf-core/mhcquant “Naked Chicken”!

nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependant (DDA) peptidomics data.

It was specifically designed to analyse immunopeptidomics data, which deals with the analysis of affinity purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines. (https://www.nature.com/articles/ncomms13404)

The workflow is based on the OpenMS C++ framework for computational mass spectrometry. RAW files (mzML) serve as inputs and a database search (Comet) is performed based on a given input protein database. FDR rescoring is applied using Percolator 3.0 based on a competitive target-decoy approach (reversed decoys). For label free quantification all input files undergo identification based retention time alignment (MapAlignerIdentification), and targeted feature extraction matching ids between runs (FeatureFinderIdentification).

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.