prep-info-file generation for amplicon

biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing

MIT License

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prep-info-file generation for amplicon #90

Closed charles-cowart closed 1 year ago

charles-cowart commented 1 year ago

Created seqpro_mf executable to perform seqpro work using amplicon mapping-files instead of sample-sheets. Currently undergoing testing against actual run-directory. unit-tests not added.

charles-cowart commented 1 year ago

@antgonza Ready for review! Many of the 19 affected files in this PR are due to the creation of an Amplicon-specific example run-directory. I created a new seqpro binary 'seqpro_mf' so I could preserve the original's command-line. However I now think I could merge them both back into a single seqpro, with a check to see if it looks like a sample-sheet or has mapping file columns and go from there.

antgonza commented 1 year ago

For reference we decided to merge this and in a future PR:

merge functionality of seqpro_mf and seqpro
add individual tests, extra from the integration tests