Fix drep add assembler flag #26
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Thank you for this PR. Everything looks good! Thank you for adding the option to skip running metaspades due to its extremely long run times. The only small suggestion I would make is related to the encoding of the megahit_only flag. Right now, True is being encoded as a 0 instead of a 1. If we flipped that, we wouldn't need to use the not statements when we are resolving/evaluating it later, and it would also be more clear as to what the value is supposed to represent. This can fixed later though.
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This is great! Thank you for adding this option to avoid running metaspades.
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| config['coassembly'] = False | ||
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| # Step 4b. Setup assembly mode | ||
| # modes: 0 - megahit + metaspades assembly | ||
| config["options"]["assembler_mode"] = "0" if sub_args.megahit_only else "1" |
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The logic here is opposite of what I would expect for a boolean flag. I see in the Snakefile you accounted for that, but would it be worth just sticking to booleans, or "1 for True" and "0 for false" to avoid ambiguity?
Address #24 , #25 , and #21