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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Update medaka commands, ready for https://github.com/artic-network/fieldbioinformatics/pull/55 #57

Closed will-rowe closed 4 years ago

will-rowe commented 4 years ago

This PR adds --medaka-model to the minion command, and updates the call to medaka consensus to set additional flags:

The default model used is r941_min_high_g351

Whilst I was there - I also added specific print statements to produce the defaults in the minion command help. This fixes https://github.com/artic-network/fieldbioinformatics/issues/27

Once this is merged, we can test and merge https://github.com/artic-network/fieldbioinformatics/pull/55