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nf-core/epitopeprediction: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

3.1.0 - Lustnau - 2025-10-22

Added

  • #304 Added --binder_only parameter to filter out non-binding peptides from the final results
  • #306 Added nf-co2footprint plugin

Fixed

  • #290 Fixed an issue where the wide format output binder column was filled falsely
  • #292 Fixed an issue with duplicated peptides in wide format output
  • #302 Fixed an issue with duplicated peptides in wide format output where metadata columns were sometimes interpreteda str or int

Dependencies

Dependency Old version New version
MultiQC 1.29.0 1.31.0
nf-core 3.2.1 3.4.1
bcftools 1.20 1.21

Changed

  • #296 Major rework of Fasta output: new header structure, full wildtype sequences, mutated peptides trimmed around mutation site in a flanking region of defined size and support for overlapping mutations.
  • #310 Drop conda support temporarily until conda lock file support is implemented

3.0.0 - Wanne - 2025-05-09

Added

  • #275 - Added bcftools/stats to add MultiQC plots for variant input
  • #279 - Add SUMMARIZE_RESULTS module and MultiQC plots. BREAKING output structure change from<outdir>/predictions/<meta.id>/<meta.id>.tsv to <outdir>/predictions/<meta.id>.tsv
  • #270 Added option --wide_format_output to provide wide format output with additional information instead of long format (default)

Changed

  • #247 - Update to nf-core template 3.0.2
  • #255 - Update to nf-core template 3.1.2
  • #250 - Implemented netmhcpan module. Removed legacy netmhc tools. Only the latest netmhcpan and netmhciipan versions will be supported (netmhcpan-4.1b, netmhciipan-4.3e)
  • #252 - Implemented netmhciipan module
  • #253 - Implemented mhcflurry module
  • #259 - Implemented mhcnuggets and mhcnuggetsii module
  • #260, #270 - Major refactoring to new, modular MHC binding subworkflow (see Meta-Issue #205). Removed legacy predictor syfpeithi. Predictors that can be specified via --tools are: mhcflurry,mhcnuggets(default),mhcnuggetsii,netmhcpan,netmhciipan. Changed --min_peptide_length and max_peptide_length to min_peptide_length_classI and --max_peptide_length_classI.
  • #263 - Rearrange supported alleles per predictor
  • #266, #268 - Refactor variant prediction with epytope
  • #282 - Update to nf-core template 3.2.1

Fixed

  • #278 - Fixed an issue where relative paths were not properly staged

v2.3.1 - Oesterberg - 2024-05-17

Changed

  • #243 - Update to nf-core template 2.14.1
  • #237 - Update to nf-core template 2.13.1

Fixed

  • #243 - Add check for protein map to prevent failure if no information is available

v2.3.0 - Oesterberg - 2024-02-26

Changed

  • #233 - Update to nf-core template 2.13
  • #228 - Update to nf-core template 2.12
  • #227 Prevent crash if no transcript is found (in splitted vcf)
  • #220 - Switch to nf-validation to parse samplesheet
  • #213 - Update epytope and Ensembl reference handling and update to nf-core template 2.10
  • #206 - Update the row checker class.
  • #203 - Update to nf-core template 2.9, rename param genome_version to genome_reference, add functionality to handle BioMart archive urls

Fixed

  • #219 - Fix `EXTERNAL_TOOLS_IMPORT`` container registry and bump version
  • #227 - Prevent crash if no transcript is found (in splitted vcf)

Removed

  • #221 - Remove support of GSvar and variant tsv input files

v2.2.1 - WaldhaeuserOst Hotfix - 2023-03-16

Fixed

  • #196 - Revert versions changes that caused bug with external tools predictions missing.

v2.2.0 - WaldhaeuserOst - 2023-03-03

Added

  • #180 - Add support for VEP annotated VCF files #172
  • #186 - Log messages from epaa.py script to stdout and provide sys.exit error messages.

Changed

  • #177 - Update to nf-core template 2.5.1
  • #178 - Update MultiQC to 1.13
  • #180 - Update to nf-core template 2.6
  • #180 - Improve runtime for VCF-based predictions
  • #187 - Update to nf-core template 2.7.1
  • #189 - Update to nf-core template 2.7.2

Fixed

  • #180 - Fix issue with frameshift determination
  • #194 - Fix software versions collection and add script licenses

v2.1.0 - Nordring - 2022-08-02

Added

  • #145 - Add functionality for handling gzipped VCF files for #143
  • #155 - Add functionality for splitting input VCF files by the number of variants #140
  • #157 - Add JSON config for external prediction tools
  • #161 - Add rank values for prediction threshold (as default) and parameter use_affinity_thresholds to use affinity thresholds instead #160
  • #165 - Add tools to full size test, add MHC class II to MHCnuggets test
  • #166 - Add support for additional non-free NetMHC family tools
  • #168 - Add parameters to specify MHC class II peptide length (max_peptide_length_class2 and min_peptide_length_class2)
  • #170 - Add binder column (binder to any specified MHC allele)

Changed

  • #152 - Update MultiQC from 1.11 to 1.12
  • #152 - Merge previous template updates up to 2.3.2
  • #153 - Update to nf-core template 2.4
  • #158 - CI tests for non-free tools are not run on PR to dev(the secret is not available there).
  • #162 - Use most recent epytope release (3.1.0)
  • #162 - Use more recent Ensembl BioMart archive release for GRCh38 (Ensembl 88)
  • #163 - Save applied tool thresholds in prediction report
  • #168 - Use MHC class information specified in sample sheet
  • #169 - Update MultiQC to 1.13

Fixed

  • #135 - Fix unique variant annotation field handling #136
  • #144 - Fix VCF file parsing #142
  • #159 - Fix execution for multiple samples of same input type

v2.0.0 - Heuberg - 2021-12-20

Added

  • #73 - Add support for the non-free NetMHC tool family including NetMHC 4.0, NetMHCpan 4.0, NetMHCII 2.2, and NetMHCIIpan 3.1
  • #83 - Add option for threshold customization
  • #101 - Add local modules for DSL2 conversion

Changed

  • #107 - Merge previous template updates up to v2.1
  • #110, #113 - Port pipeline to Nextflow DSL2 syntax
  • #114 - Update python 2.7 to python 3.8.9 in split_peptides.nf and merge_json.nf.
  • #117 - Bump minimal NXF version to 21.10.3
  • #121 - Extend full test to cover more test cases
  • #122 - Update to nf-core template v2.2
  • #123 - Remove support for outdated external tools NetMHCII 2.2 and NetMHCIIpan 3.1

Fixed

v1.1.0 - Morgenstelle - 2020-10-20

Added

  • #58 - Add tests for MHCnuggets and MHCflurry
  • #57 - Add option (--fasta_output) to write out FASTA file with protein sequences
  • #45 - Add test for FASTA input
  • #44 - Add parameter (--show_supported_models) to write out supported models in files
  • #44 - Add check if requested models for specified tools are supported by FRED2
  • #42 - Add support for FASTA files with protein sequences as input (--input)
  • #31 - Add support for mouse alleles
  • #30 - Add parameter (--mem_mode) to change between different memory modes
  • #29 - Add parallelisation for peptide input

Changed

  • #59 - Parse and store metadata dynamically for variant data
  • #50 - Change parameter to specify the genome version to --genome_version ( --genome deprecated)
  • #50 - Merge template updates (v1.10.1, and v1.10.2)
  • #47 - Update FRED2 to version 2.0.7
  • #35 - Merge template updates (v1.9)
  • #30 - Set maxRetries from 1 to 3

Fixed

  • #56 - Fix result output for more than one prediction method #55
  • #53 - Fix score and affinity output of MHCnuggets and MHCflurry #32
  • #52 - Fix MHCflurry permission problem when run with docker profile #51
  • #39 - Fix display of prediction tool version #36

v1.0.0 - purple-nickel-shrimp - 2019-12-05

  • Initial release of nf-core/epitopeprediction, created with the nf-core template.