Genome Updater Versions Save

• 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

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

Support the latest GTDB release R214

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

Bug fixes with invalid URLs and GTDB MD5SUM file #78

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

• 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

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

• 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

• stable code
• better parameter for taxonomic id and top assemblies selection
• testing with bats https://github.com/bats-core/bats-core
• curl support
• custom filter support
• many smaller bug fixes and improvements