Revisit legacy fastq file search code #112

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charles-cowart opened this issue Feb 25, 2025 · 0 comments

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charles-cowart commented Feb 25, 2025 •

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This is legacy code in FastQCJob and MultiQCJob:

https://github.com/charles-cowart/mg-scripts/blob/dd39ff0a1b59ecb6def1f0cd17194f32d783de60/sequence_processing_pipeline/FastQCJob.py#L85-L139

Look into possibly revising it using glob(), walk() or otherwise make it more compact.

Revisit other areas that involve zero_files directories and 'only-adapter-trimmed' as well.

Consider adding assumptions expressed in comments into the glob statement:
https://github.com/charles-cowart/mg-scripts/blob/5c19f8d42275140ab915b8de62f0501c1f3198c3/sequence_processing_pipeline/NuQCJob.py#L580

charles-cowart mentioned this issue

Omnibus PR qiita-spots/mg-scripts#163

Merged

antgonza transferred this issue from qiita-spots/mg-scripts

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