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Version 0.3.0

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@GallVp GallVp released this 30 Apr 01:19
· 229 commits to main since this release
0.3.0
18dc82c

What's Changed

Commit history: v0.2...0.3.0

Added

  1. Added changelog and semantic versioning
  2. Changed license to MIT
  3. Updated .editorconfig
  4. Moved .literature to test/ branch
  5. Renamed pangene_local to local_pangene
  6. Renamed pangene_pfr to pfr_pangene
  7. Added versioning checking
  8. Updated github workflow to use pre-commit instead of prettier and editorconfig check
  9. Added central singularity cache dir for pfr config
  10. Added SORTMERNA_INDEX before SORTMERNA
  11. Fixed sample contamination bug introduced by file.simpleName
  12. Now using empty files for stub testing in CI
  13. Now BRAKER can be skipped by including BRAKER outputs from previous runs in the target_assemblies param
  14. Added gffcompare to merge liftoff annotations
  15. Renamed samplesheet param to fastq
  16. Now using assemblysheet in combination with nf-validation for assembly input
  17. Added nextflow_schema.json
  18. Now using nf-validation to validate fastqsheet provided by params.fastq
  19. Moved manifest.config and reporting_defaults.config content to nextflow.config
  20. Now using a txt file for params.external_protein_fastas
  21. Now using nf-validation for params.liftoff_annotations
  22. Now using nf-validation for all the parameters
  23. Added PURGE_BREAKER_MODELS sub-workflow
  24. Added GFF_EGGNOGMAPPER sub-workflow
  25. Now using a custom version of GFFREAD which supports meta and fasta
  26. Now using TSEBRA to purge models which do not have full intron support from BRAKER hints
  27. Added params eggnogmapper_evalue and eggnogmapper_pident
  28. Added PURGE_NOHIT_BRAKER_MODELS sub-workflow
  29. Now merging BRAKER and liftoff models before running eggnogmapper
  30. Added GFF_MERGE_CLEANUP sub-workflow
  31. Now using description field to store notes and textual annotations in the gff files
  32. Now using mRNA in place of transcript in gff files
  33. Now eggnogmapper_purge_nohits is set to false by default
  34. Added GFF_STORE sub workflow
  35. external_protein_fastas and eggnogmapper_db_dir are not mandatory parameters
  36. Added contributors
  37. Add a document for the pipeline parameters
  38. Updated pfr_pangene and pfr/profile.config
  39. Now using local tests/stub files for GitHub CI
  40. Now removing iso-forms left by TSEBRA using AGAT_SPFILTERFEATUREFROMKILLLIST
  41. Added pyproject.toml
  42. Now using PFAMs from eggnog if description is '-'

Fixed

  1. Removed liftoff models with valid_ORF=False
  2. Updated license text to include 'Copyright (c) 2024 The New Zealand Institute for Plant and Food Research Limited'

Dependencies

  1. NextFlow!>=23.04.4
  2. nf-validation=1.1.3

Deprecated

Assets 2
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