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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 code to allow medaka to automatically detect base caller model. #153

Closed LeeBergstrand closed 2 months ago

LeeBergstrand commented 2 months ago

All Medaka model parameter in the config to auto. Medaka will then parse the FASTQ/BAM to get the base caller mode.

Addresses issue https://github.com/rotary-genomics/rotary/issues/97

LeeBergstrand commented 2 months ago

@jmtsuji Ready for review. I have tested this with auto and with specified base caller models.