assembly_finder v0.3.0

Summary

• Simplified assembly_finder cli
• Added checksum verification
• Split summary table into three tables for sequence, assembly and taxonomy summary
• Allow different parameters (assembly status, refseq category ...) for each entry
• Improvements and bugfixes

Details

Additions

• 25e7f05 81efbf6 Added sequencing technology, organism name, Biosource submission types in assembly table
• 81efbf6 Added sequence table to have sequence info (header to taxid correspondance)
• 81efbf6 Added taxonomy table to have linear taxonomy info
• 12dfee4 Allow for different assembly search parameters for each entry
• dbca07a Added sha256 checksum verification
• 5907660 56a0389 Added taxa.sqlite rules and option to avoid saving it in the conda env

Changes

• 81efbf6 Split summary table into three tables for sequence, assembly and taxonomy summary
• 12dfee4 Changed sort priority to refseq category then assembly status, followed by coverage and N50
• a17e3a1 Improved directory structure (moved scripts to bin directory)
• cb1f4af Removed run sub-command for simpler cli
• 25e7f05 Renamed summary table headers (no more CamelCase !)
• 43a8d0e Removed required NCBI email and key
• 2335ea7 Removed wget option
• 8c947f4 Updated dependency versions

Fixes

• 6f43cd7 Fixed number of assembly selection with or without rank filtering