- 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.