v1.0

v1.0 - November 30, 2023

Added

• Automate phylogenomic analysis from ppanggolin outputs (d78dfc9)
• Add parameter to skip pangenomics/phylogenomics subworkflow (3f3f5b2)
• Add new ARETE logo (4a3b492)
• Added --annotation_tools parameter (2cf57a3)
• Validate sample IDs in annotation input check (09400c0)
• General improvements to documentation (3bdea30, 21b853b, a109c3c, a10f7bd)
• Add phylogenomics entry (1cb6563)
• Add recombination subworkflow (1d10d96)
• Add QC assembly filtering (ccc2f50)
• Improve MultiQC reports (b097f9b)
• Add rSPR (b0d0cf1, 7e494ab)
• Add entries for EvolCCM and recombination (8bdad86, 710ba25)
• Add Gene Order (6b7e268, b22988b)

Fixed

• Stop ppaggoolin from altering input file (53cbe77)
• Return PopPUNK create db outputs (339620c)
• Fix large dataset error on rSPR entry (9a119b4)

Deprecated

• No longer includes phispy information in the annotation report (82bb3f8)