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@GallVp GallVp released this 06 Oct 21:33
· 88 commits to main since this release
0.4.0
24a8f50
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What's Changed

Added

  1. Added orthofinder_annotations param
  2. Added FASTA_GFF_ORTHOFINDER sub-workflow
  3. Added evaluation by BUSCO #41
  4. Included common tax ids for eggnog mapper #27
  5. Implemented hierarchical naming scheme: geneI.tJ, geneI.tJ.exonK, geneI.tJ.cdsK #19, #34
  6. Now sorting list of bam and list of fastq before cat to avoid resume cache misses
  7. Allowed BAM files for RNA evidence #3
  8. Added GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES sub-workflow for splice type statistics #11
  9. Changed orthofinder_annotations from FASTA/GFF to protein FASTA #43
  10. Added param enforce_full_intron_support to turn on/off strict model purging by TSEBRA #21
  11. Added param filter_liftoff_by_hints to evaluate liftoff models with TSEBRA to make sure they have the same level of evidence as BRAKER #28
  12. Added a script to automatically check module version updates
  13. Reduced BRAKER3 threads to 8 #55
  14. Now the final annotations are stored in the annotations folder #53
  15. Now a single fasta file can be directly specified for protein_evidence
  16. eggnogmapper_db_dir is not a required parameter anymore
  17. eggnogmapper_tax_scope is now set to 1 (root div) by default
  18. Added a test profile based on public data
  19. Added parameter add_attrs_to_proteins_fasta to enable/disable addition of decoded gff attributes to proteins fasta #58
  20. Added a check for input assemblies. If an assembly is smaller than 1 MB (or 300KB in zipped format), the pipeline errors out before starting the downstream processes #47
  21. Now REPEATMASKER GFF output is saved via CUSTOM_RMOUTTOGFF3 #54
  22. Added benchmark column to the input sheet and used GFFCOMPARE to perform benchmarking #63
  23. Added SEQKIT_RMDUP to detect duplicate sequence and wrap the fasta to 80 characters
  24. Updated parameter section labels for annotation and post-annotation filtering #64
  25. Updated modules and sub-workflows

Fixed

  1. Fixed BRAKER spellings #36
  2. Fixed liftoff failure when lifting off from a single reference #40
  3. Added versions from GFF_STORE sub-workflows #33

Dependencies

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

Deprecated

  1. Renamed external_protein_fastas param to protein_evidence
  2. Renamed fastq param to rna_evidence
  3. Renamed braker_allow_isoforms param to allow_isoforms
  4. Moved liftoffID from gene level to mRNA/transcript level
  5. Moved version_check.sh to .github/version_checks.sh
  6. Removed dependency on https://github.com/kherronism/nf-modules.git for BRAKER3 and REPEATMASKER modules which are now installed from https://github.com/GallVp/nxf-components.git
  7. Removed dependency on https://github.com/PlantandFoodResearch/nxf-modules.git
  8. Now the final annotations are not stored in the final folder
  9. Now BRAKER3 outputs are not saved by default #53 and saved under etc folder when enabled
  10. Removed local profile. Local executor is the default when no executor is specified. Therefore, the local profile was not needed.
  11. Removed CUSTOM_DUMPSOFTWAREVERSIONS

Full Changelog: 0.3.3...0.4.0

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