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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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Flag renaming for clarity #25

Closed Astahlke closed 2 years ago

Astahlke commented 3 years ago

I was confused about how to direct the pipeline to skip 02_Arrow if the Falcon assembly has already been polished. Currently you would supply --falcon-unzip True to skip to purge_dups. I suggest that --falcon_unzip be changed to falcon_polish for clarity.

I think there may be some other renaming, eg steptwo that could be more clear as well.

j23414 commented 3 years ago

Yes, and --step 1 and --step 2. I'll make these flag-y changes on the "edits_2021" branch. Want to run some tests before merging.