nf-core/epitopeprediction: Changelog

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

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`

#125, #126 - Fix AWS test

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.