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Commits on Mar 26, 2026

• Release v0.3.8

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• Merge pull request #72 from ylab-hi/fix/malformed-params-and-string-comparison

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• Add CHANGELOG entry for PR #72

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• Fix malformed params string and is-not string comparisons

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• Merge pull request #60 from ylab-hi/refactor/standardize-log-paths

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• Standardize log paths and fix missing log redirects across all rules

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• Remove stale [0.5.x] placeholder section from CHANGELOG

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• Merge pull request #58 from ylab-hi/fix/batch-binding-affinity-predictions

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• Add CHANGELOG entry for PR #58 (batch binding affinity predictions)

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Commits on Mar 25, 2026

• batch large FASTA inputs for binding affinity predictions

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Commits on Nov 1, 2025

• changes to v0.3.7 added

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• sort reads by QNAME before splitting in MHC-I genotyping (#57)

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Commits on Oct 31, 2025

• fixed bug with wrong perl path (in MHC-II IEDB BA call) (#56)

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• mhc_ii modified prediction files

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Commits on Oct 29, 2025

• Changes to mhc-II prediction (#55)

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Commits on Apr 5, 2025

• removed link

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• updated citation badge

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• citation badge

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• added requirements to become basic snakemake workflow

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• add missing genotyping file

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• fixed filtering SE reads (#52)

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Commits on Apr 2, 2025

• added changes for v0.3.3

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• fixed align parameters in basic-config as these were remnants from an older version (#51)

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Commits on Apr 1, 2025

• added instruction for testing installation

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Commits on Mar 30, 2025

• Processing of bamfiles for MHCII (#49)

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Commits on Mar 29, 2025

• return to unspecified pysam

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• Resolve Issues with MHCII typing and workflow with custom files (#48)

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Commits on Mar 12, 2025

• added note for relative paths in config

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Commits on Sep 2, 2024

• remove apptainer environment

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• update description to similarity names

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• renamed protein and pathogen fields

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Commits on Aug 31, 2024

• updated scanexitron

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• commit badge

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• fork badge

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• corrected link

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