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

genome_updater v0.5.2

Bug fixes with invalid URLs and GTDB MD5SUM file #78

genome_updater v0.5.1

General bug fixes. Thanks to @shenwei356 for reporting and fixing.

genome_updater v0.5.0

• Keep track of arguments inside repository (updates can be done with -o only)
• Full GTDB r207 support and full taxonomy integration / filtering options with -A and -T
• Taxonomy support for ncbi and gtdb with -M
• Rank based top assemblies -A 3 for top 3 for each leaf node or -A genus:3 for top 3 for each genus
• Some parameters were updated or merged:

 -z       > >    -M gtdb
 -S/-T    > >    -T
 -P/-A    > >    -A

• Sequence and assembly reports are generated by timestamp (before was one per label)
• Many other fixes and improvements

genome_updater v0.4.1

• Removed default database (refseq), -d must be provided
• New debug mode -Z (changed from -D)
• small code improvements and bugs fixes

genome_updater v0.4.0

• set up version before downloading when updating #44
• keep history of usage documented with history.tsv
• filter by date #42
• rollback/branch option -B
• retry to download in batches option -R
• general improvements and bug fixes