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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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synDNA notebook update #145

Closed RodolfoSalido closed 1 year ago

RodolfoSalido commented 1 year ago

added absolute quant functionality to the iSeqnorm notebook. The test data does not use the new functionality, but the samplesheet includes the new column.

charles-cowart commented 1 year ago

@RodolfoSalido I think @mmbryant23 might want to review it at some point, but it looks good to me. The only thing I would ask to fix is the header numbering around the change, which is quite confusing. Here's the headers around the change, in order:

2.3. Step 3: calculate normalization volumes and add to plate map Step 3b (optional): reformat plate or add synDNA spike-in 2.5. Add synDNA spike-in 2.6. Step 4: make pick list 2.7. Step 5: write pick list to file

I think maybe changing Step 3b to be 2.4 might be an option? Or keeping it as-is and decrementing 2.5-2.7 by .1. Another thing I want to make sure of is that this notebook does several things, and Step is reset to 1 more than once. Perhaps Step 3b should be the start of a new Step 1?

charles-cowart commented 1 year ago

@RodolfoSalido One additional item: It looks like your tests are passing, but your code is not passing flake8 for style. The easiest way I know of to correct for this is to install flake8 into your environment with 'pip install flake8' and type 'flake8 metapool' on the command-line. This will bring up a list of line numbers and messages for everything flake8 doesn't agree with.

If it's a lot, you can type 'flake8 metapool | head' and this will limit it to the first ten; just make sure you run it again afterward to catch additional errors! :)

RodolfoSalido commented 1 year ago

I will work on improving the header numbering. I think we stopped paying close attention to it, but it would be beneficial to improve it to a state that makes sense.

Will also work on flake8 styling fixes.

charles-cowart commented 1 year ago

I will work on improving the header numbering. I think we stopped paying close attention to it, but it would be beneficial to improve it to a state that makes sense.

Will also work on flake8 styling fixes.

Thanks Rodolfo! :)

RodolfoSalido commented 1 year ago

While we wait for McKenzie to come back and review, I'll also consult with the wetlab to see if they have any feedback on the new modules.

charles-cowart commented 1 year ago

@mmbryant23 @RodolfoSalido @antgonza Bumping to keep this PR in everyone's short-term memory.