Batch option for Medaka

[Spiltz]

Batch option for Medaka

[rpetit3]

This should be available in v1.0.13 (https://github.com/rpetit3/dragonflye/releases/tag/v1.0.13). I'll get it updated on Bioconda soon.

Thank you very much for the suggestion @Spiltz !

Please feel free to reopen if it doesn't work as expected!

[rpetit3]

Yeah, I think I can get it added, unfortunately won't be able to test (no gpu to test on).

Are you thinking something like --batch_size INT at runtime?

[Spiltz]

Yes exactly.
medaka call would look something like this:
run_cmd("medaka_consensus -i $FINAL_READS -d $POLISHED_FASTA -o $polish_dir -m $model -b $batch_size -t $cpus 2>&1", "polishing - medaka ($i of $medaka)");

Default batch size is 200.

[rpetit3]

Do you think a --medaka_opts might be more useful so that you can have access to change any other parameters in medaka?

[Spiltz]

Sure, adds quite a lot of flexibility there. Also prevents introducing code to check for --batch_size non-empty

[rpetit3]

Awesome! I'll get this added for you. Will update soon

[rpetit3]

Hopefully this does it for you: 79686e6

if tests pass, I'll submit a new release.