Version 0.6.0

What's Changed

Added

1. Added cDNA and CDS outputs to <OUTPUT_DIR>/annotations/ directory #118
2. Added parameter add_attrs_to_proteins_cds_fastas
3. Added parameter filter_genes_by_aa_length with default set to 24 which allows removal of genes with ORFs shorter than 24 #125

Fixed

1. Fixed an issue where TSEBRA failed because LIFTOFF lifted non-protein coding genes #121
2. Switched branch name from master to main in the GHA CIs
3. Fixed an issue in genepal_report.Rmd which caused the pangene matrix plot to fail when the number of clusters exceeded 65536 #124
4. Fixed an issue where GENEPALREPORT process failed due to OOM kill signal from SLURM #123
5. Fixed an issue where Gff merge after liftoff failed when one of the Gff files did not contain any genes
6. Fixed an issue where gxf_fasta_agat_spaddintrons_spextractsequences crashed due to short introns #89

Dependencies

1. Nextflow!>=24.04.2
2. nf-schema@2.1.1

Deprecated

1. Removed parameter add_attrs_to_proteins_fasta

PRs

• Add gffread EXTRACT_CDNA and EXTRACT_CDS feature to outputs by @liamlelievre in #119
• Fixed TSEBRA failure issue by @GallVp in #122
• Fixed issues in genepal-report by @GallVp in #126
• Added parameter filter_genes_by_aa_length by @GallVp in #127
• Fixed post-liftoff merge by @GallVp in #130
• Fixed a crash due to short introns by @GallVp in #131
• Release candidate for 0.6.0 by @GallVp in #129

New Contributors

• @liamlelievre made their first contribution in #119

Full Changelog: 0.5.0...0.6.0