Changed

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

Fixed

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

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

Fixed

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

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

Added

#145 - Add functionality for handling gzip VCF files for #143 #166 - Add support for additional non-free NetMHC family tools #161 - Add rank values for prediction threshold and parameter use_affinity_thresholds to use affinity thresholds instead #160

Changed

#162 - Use most recent epytope release (3.1.0) #168 - Use MHC class information specified in sample sheet

Fixed

#135 - Fix unique variant annotation field handling #136 #144 - Fix VCF file parsing #142

See CHANGELOG for more information.

Added

#73 - Add support for the non-free NetMHC tool family #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 21.10.4 #121 - Extend full test to cover more test cases #122 - Update to nf-core template v2.2 #123 - Remove support for outdated external tools

Fixed

#125, #126 - Fix AWS test

See CHANGELOG for more information.

Added

#57 - Add option (—fasta_output) to write out FASTA file with protein sequences #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) #47 - Update FRED2 to version 2.0.7

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

See CHANGELOG for more information.

nf-core/epitopeprediction V 1.0.0 - “Purple Nickel Shrimp”

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