genome_updater v0.8.1

Small bug fix GTDB latest taxonomy filename

genome_updater v0.8.0

Changed:

• -H hard (default) keeps files between versions as hard links. -H soft to get previous behavior. #103
• -N is now -N split (default) to store files in sub-folders. -N flat to get previous behavior.
• Remove extra file checks by default. Extra file check can still be done in a dry-run -x -k.

New:

• Add versioning to GTDB taxonomy integration with -M, e.g.: gtdb-220
• New option to check for gzipped file integrity -G
• General bug fixes and improvements

Thanks to @mbhall88 for the contribution!

genome_updater v0.7.2

Fix download #104

genome_updater v0.7.1

Fix date filtering due to the change of the date separator from "/" to "-" #102

genome_updater v0.7.0

• improve and extend custom filters -F docs #75
• allow negation in taxonomy -T with ^ docs #89
• defaults GTDB url to a "faster" source code #99
• allow local taxdump as input docs
• include shellcheck in the CI

genome_updater v0.6.4

Removed "representative genome" from RefSeq category parameter since it is now deprecated by NCBI in favor of "reference genome": https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/25/updated-terminology-reference-genome/

Thanks to @ktmbiome-niaid for reporting it.

genome_updater v0.6.3

• Adapt to new assembly_summary.txt format (38 columns instead of 23), as reported #86
• Skip MD5SUM from GTDB files due to inconsistencies, reported here: https://forum.gtdb.ecogenomic.org/t/md5sum-txt-not-matching-filenames-on-latest/486

genome_updater v0.6.2

• fix bug with older find versions (<=4.6.0)

genome_updater v0.6.1

Support the latest GTDB release R214

genome_updater v0.6.0

• -N to save files in the NCBI ftp folder structure
• general infrastructure fixes and improvements