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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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Fixes bug in make_sample_sheet() #151

Closed charles-cowart closed 11 months ago

charles-cowart commented 11 months ago

Fixes bug in make_sample_sheet() when contains_replicates field is added to Bioinformatics metadata. Adds synDNA pool number column to Finrisk 33-36_plate_map.tsv so that metagenomics_samplesheet_generator.ipynb functions properly.

RodolfoSalido commented 11 months ago

Looks good. I'll try to cleanup the notebooks so that all of the newer updates (plate replicates & synDNA spike-in) are properly incorporated into the workflow that the wetlab performs.

RodolfoSalido commented 11 months ago

can we merge this ?

charles-cowart commented 11 months ago

can we merge this ?

Is it blocking you? I ask because @antgonza and @mmbryant23 haven't replied yet. It'd be nice to wait for their responses but if it's holding you back then that's something different, IMHO.

RodolfoSalido commented 11 months ago

Maybe I'm overseeing a simple fix, but I'm trying to generate a sample_sheet that contains replicates, but I can't because this commit hasn't been merged. Is there a simpler way for me to pull this branch before it gets merged?

charles-cowart commented 11 months ago

Maybe I'm overseeing a simple fix, but I'm trying to generate a sample_sheet that contains replicates, but I can't because this commit hasn't been merged. Is there a simpler way for me to pull this branch before it gets merged?

I'm just going to merge it - we can always pull out the XLS spreadsheet if need-be as a separate issue. This is really meant to just be a bug fix PR.

charles-cowart commented 11 months ago

@RodolfoSalido Thank you for your patience Rodolfo! Please feel free to pull from the master branch!