epitopeprediction - 3.0.0 - Wanne - 2025-05-09

Added

• #275 - Added bcftools/stats to add MultiQC plots for variant input

Added

• #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

- Nextflow
Published by jonasscheid 10 months ago

epitopeprediction - v2.3.1 - Oesterberg - 2024-05-17

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

- Nextflow
Published by jonasscheid almost 2 years ago

epitopeprediction - 2.3.0 - Oesterberg

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

- Nextflow
Published by jonasscheid about 2 years ago

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

Fixed

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

- Nextflow
Published by ggabernet almost 3 years ago

epitopeprediction - 2.2.0 - WaldhaeuserOst

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

- Nextflow
Published by ggabernet almost 3 years ago

epitopeprediction - 2.1.0 - Nordring

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.

- Nextflow
Published by christopher-mohr over 3 years ago

epitopeprediction - 2.0.0 - Heuberg

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.

- Nextflow
Published by christopher-mohr about 4 years ago

epitopeprediction - 1.1.0 - Morgenstelle

Added

57 - Add option (--fasta_output) to write out FASTA file with protein sequences

44 - Add parameter (--showsupportedmodels) 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.

- Nextflow
Published by christopher-mohr over 5 years ago

epitopeprediction - nf-core/epitopeprediction V 1.0.0 - "Purple Nickel Shrimp"

nf-core/epitopeprediction V 1.0.0 - "Purple Nickel Shrimp"

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

- Nextflow
Published by apeltzer about 6 years ago