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rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Add download command #175

Closed LeeBergstrand closed 3 months ago

LeeBergstrand commented 4 months ago

Add code to enable a Rotary download command to pre-download all databases required by rotary and prepare them for later use.

Addresses issue https://github.com/rotary-genomics/rotary/issues/45

LeeBergstrand commented 4 months ago

@jmtsuji Tested with dry run be feel free to review.

LeeBergstrand commented 4 months ago

@jmtsuji Tested with dry run be feel free to review.

Tested with a full run. It works. Note that it will create benchmarking and log folders in the CWD.

jmtsuji commented 3 months ago

@jmtsuji Tested with dry run be feel free to review.

Tested with a full run. It works. Note that it will create benchmarking and log folders in the CWD.

Great that this is tested and working! 👍 Creating the benchmarking and log folders in the CWD seems OK for now. Long-term, we could consider adding a flag to specify the working dir for the download module, but I don't think this is urgent.

LeeBergstrand commented 3 months ago

@jmtsuji Decided to remove the CLI config flag. I originally had this so the user could specify what databases to download. However, after reviewing my code my code ignores those config changes and downloads everything anyways. I decided to remove the config cli parameter to make things simpler.