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chanzuckerberg / idseq-workflows

Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
31 stars 12 forks source link

Replace RunStar in host filter #139

Closed rzlim08 closed 3 years ago

rzlim08 commented 3 years ago

This might be a bit of a heavy PR. I pulled some of the functions out of idseq-dag and put them into idseq_utils in order to make them standalone functions. As this matures, we may will want to make this into a separate repository.

The current tests and benchmarks seem to pass, I'm still making new ones to cover the different cases.

rzlim08 commented 3 years ago

One design note. I see that you are calling the utils like a binary from bash. What are your thoughts about calling them via python like?

python3 <<< CODE
    from idseq_utils import foo

    foo(~{some_thing})
CODE

I think this is a great idea! I didn't think of it, but it would probably be better than the current solution. I'll see if I can convert this.

rzlim08 commented 3 years ago

@morsecodist

The python scripts should have been replaced by inline code here. I haven't replaced the read_descriptions util, as I think it may be better to rethink/rewrite our descriptions in general.