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cutadapt_report should not need to be defined in 2 locations #38

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nsheff opened this issue Aug 22, 2019 · 1 comment
Open

cutadapt_report should not need to be defined in 2 locations #38

nsheff opened this issue Aug 22, 2019 · 1 comment
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@nsheff
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nsheff commented Aug 22, 2019

we need a way to specify all the locations and then just use them, instead of defining them in functions and then again outside of functions:

    cutadapt_folder = os.path.join(outfolder, "cutadapt")
    cutadapt_report = os.path.join(cutadapt_folder, args.sample_name + "_cutadapt.txt")
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nsheff commented Aug 26, 2019

Related to: pepkit/looper#201

I think this will wait to be solved by some new infrastructure in dealing with sample attributes in looper/pipeline interface:

pepkit/looper#216

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