Calling binny within an existing snakemake pipeline

[EisenRa]

G'day, I recently read the preprint and am keen to try out binny.

I'd like to implement it within an existing snakemake pipeline that I developed, which already handles sample inputs, assembly, mapping etc. I see that binny calls snakemake, and requires a config file to run, so I'm wondering whether it's possible to call binny like other binners (e.g. semibin single_easy_bin -i 'assembly.fasta' -b 'sample.bam' -o 'outputdir')?

Cheers,
Raphael

[ohickl]

Hi Raphael,

you could implement it as a Snakemake Module like e.g. here (bit experimental) or have rules that would handle the setup and config file generation with a final rule calling the binny wrapper with the generated config.
I will work on an updated wrapper that will allow calls directly specifying arguments like your example. Hopefully ill get to it soon.

Best

Oskar

[EisenRa]

Hi Oskar,

Thank you for the quick response! Great, I think I will wait for the updated wrapper :-). Feel free to reach out if I can help with testing.

Cheers,
Raphael