The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- 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
- Create only one decoy database #299
- Template update 2.11 #300
- Template update 2.12 #303
- Use
groupKeyto streamline group-wise processing #310 - Replace
PYOPENMS_IDFILTERwithOPENMS_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
- Set identification mode as default and rename
--skip_quantificationto--quantify#323
- Removed MS²PIP and DeepLC modules. These feature generators are now called via the MS²Rescore framework #293
- Support for brukers tdf format by adding tdf2mzml converter #263
- DeepLC retention time prediction
- MS2PIP peak intensity prediction
- 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
- Optimize resource allocations
- Template update 2.9 #274
- Improved quantification such that merged FDR-filtered runs can be quantified properly
- Template update 2.10 #282
- #266 Switched from OpenMS version 2.8.0 to newest version 3.0.0 #265
- #266 Bumped ThermoRawFileParser version from 1.4.0 to 1.4.2
- OpenMS RT prediction
- Added low resolution settings (e.g. Iontrap) #254
- Increased comet search, through altering the spectrum_batch_size from 500 to 0
- #249 - nf-core template update (version 2.7.2)
- #258 - Adjusted decoy strategy to reverse #255 and made consistent fdr-level flags #228
- #845 - Adjusted nf-core test data set #233
Initial release of nf-core/mhcquant, created with the nf-core template.
- Additional output from
CometAdapter(generated with the parameter--pin_out) - Folder structure within the
intermediate_resultsfolder to retrace the outcome files easier OPENMS_FALSEDISCOVERYRATEandOPENMS_IDFILTER_FOR_ALIGNMENTare 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
assetsfolder - #229 Add ion annotation feature requested in #220
- #235 Add the
annotate_ionsparameter to enable/disable the ion annotation feature (default is false)
- 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_QUANTIFICATIONis renamed toMAP_ALIGNMENTto indicate that the alignment (and the complementing processes) of the different maps happens herePOST_QUANTIFICATIONis renamed toPROCESS_FEATUREsince the feature identification and processing is done here- Outcome of
OPENMS_FEATUREFINDERIDENTIFICATIONgot lost during one of the previous updates, this is reintroduced OPENMS_TEXTEXPORTER_UNQUANTIFIEDandOPENMS_TEXTEXPORTER_QUANTIFIEDreturn 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_sheetparameter
- 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 |
OPENMS_TEXTEXPORTER_PSMSwas removed due to the outcome of the comet adapter step
- #210 - Icons to the different parameters in the
nextflow_schema.json
- #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
- #206 Updated the workflow picture
- Adjustments of the
PRE_QUANTIFICATIONsubworkflow:OPENMS_FALSEDISCOVERYRATE,OPENMS_IDFILTER_FOR_ALIGNMENT, andOPENMS_TEXTEXPORTER_SINGLE - Included
OPENMS_TEXTEXPORTER_UNQUANTIFIEDto write a combined FDR filtered output file for unquantified data - Included
pipeline summaryand increment thedocumentationparagraph - #195 Updated parameter documentation
- #189 Added backslashes in Quick Start in README
- #188 Added reference links to README
- 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
| Dependency | Old version | New version |
|---|---|---|
MultiQC |
1.11 | 1.12 |
- #191 Removed the table of contents from usage.md
- 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
- 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)
| Dependency | Old version | New version |
|---|---|---|
fred2 |
2.0.6 | 2.0.7 |
- 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 typos
- [#165] - Raise memory requirements of FeatureFinderIdentification step
- [#176] - Pipeline crashes when setting the --skip_quantification flag
Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
| 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 |
NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.
DSL1 to DSL2 conversion
- Different processes based on a unique step in the pipeline
- Inclusion of one sub workflow: refine fdr on predicted subset
- The process: openms_cometadapter includes commented lines (which could be used as a reference for future module development)
- MHCquant pipeline is ran from workflows/mhcquant.nf instead of main
- Template update to nf-core tools version 2.1
- Template raise to 1.10.2
- Added parameter json schema
- Added full size AWS test profile
- Included new parameters for Neutral loss and precursor ion inclusion
- Changed trigger for AWS tests
- set optimal config for cluster execution
- fix duplication of ids / mixing of channels
- integrate sample, allele and vcf sheets instead of file dirs
- branched mzML/raw input
- introduce param to skip quantification
- raise OpenMS version to 2.5
- adapt workflow accoringly with new options
- remove specifying input as file dirs eg "data/*.mzML"
- Raw File Reading
- RT prediction
- Quantification FDR
- Variant pass filter
- nf-core template update 1.8 and 1.9
- Added version numbers of mhcnuggets and Fred2
- output file order in intermediate results
- increased run times for MS search and variant translation
- nf-core template update
- x,z,a,c ions
- quantification fdri
- empty neoepitope list bugs fixed
- documentation
- scrape version numbers
- MHCnugget predictor
- Few fixes
- RT features for percolator
- linear retention time alignment
- refine_fdr README
- sort channels by basename
- fixed psm-level-fdrs
- fixed refine_fdr_on_predicted_subset float error
- filter out uncommon aminoacids U,X,B,J,Z
- default params to false
- change on centroidisation parameter
- small changes on docu
- process identical names bug
- Subset FDR refinement option
- Fred2 dependency
- vcf parser and translation to proteins
- Documentation
- optional mhcflurry binding predictions
- peak picking as optional preprocessing step
- adapted a few parameters such as the default fdr threshold
- updated documentation
- Initial release of nf-core/mhcquant, created with the nf-core template.