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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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Incorporating new samplesheet generation scheme into wetlab notebooks. #158

Closed RodolfoSalido closed 7 months ago

RodolfoSalido commented 7 months ago

Changed the wetlab notebooks to incorporate the new samplesheet generation process with SheetType and SheetVersion.

RodolfoSalido commented 7 months ago

@wasade

charles-cowart commented 7 months ago

Hi @RodolfoSalido . I fixed the fix so that all of the tests work again. make_sample_sheet() returned an error which I was able to resolve but I need you to replace the values with meaningful ones. Specifically, I changed vol_extraction_elution_ul to vol_extracted_elution_ul, but mass_syndna_input_ng and extracted_gdna_concentration_ng_ul are indeed missing in the plate_df you're passing to make_sample_sheet(). This may be as simple as 'git add'ing './test_output/QC/YYYY_MM_DD_Celeste_Adaptation_df.txt' to the PR if you've already modified it. Please review everything in the notebook between CHARLIE_ADDED and END_CHARLIE_ADDED.

plate_df['vol_extracted_elution_ul'] = 70

CHARLIE ADDED

plate_df['mass_syndna_input_ng'] = 100 plate_df['extracted_gdna_concentration_ng_ul'] = 100

END CHARLIE ADDED

AmandaBirmingham commented 7 months ago

Haven’t been following all of this so maybe I’m missing context but: those two columns are definitely NOT optional for abs_quant_metag sample sheets. However, they would be inappropriate for “standard_metag” spreadsheets, even as optionals.

From: Charles Cowart @.> Date: Tuesday, December 12, 2023 at 11:23 AM To: biocore/metagenomics_pooling_notebook @.> Cc: Subscribed @.***> Subject: Re: [biocore/metagenomics_pooling_notebook] Incorporating new samplesheet generation scheme into wetlab notebooks. (PR #158)

@charles-cowart commented on this pull request.

In notebooks/metagenomics_pipeline_iSeqnorm.ipynbhttps://urldefense.com/v3/__https:/github.com/biocore/metagenomics_pooling_notebook/pull/158*discussion_r1424478747__;Iw!!LLK065n_VXAQ!mPspicbCS6usemsV5AuMyDKnZaWdMURFo2X4JII2YeVGFvtu1KSrsqCgw4LT2_d066GDfV5BvHKscxqBFzcRzXnCs_AE$:

  • "# CHARLIE ADDED\n",

Hmm, this is troublesome since the metadata directs make_sample_sheet() to create an AbsQuantSampleSheetv10() object, which requires those two columns. I don't mind if they're empty, but as of now they do need to be present. I'm confused because it sounds like these two columns are suddenly optional, and I have no information on how to treat them.

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RodolfoSalido commented 7 months ago

@AmandaBirmingham the issue you raised was addressed. The notebook that Charlie was running was essentially not including the synDNA columns because it's designed to default to a standard_metag workflow (which doesn't include the extra columns when tracking information associated with samples). That's why he added those columns manually right before running make_sample_sheet(). I corrected the manual additions and tested that the abs_quant workflow and the make_sample_sheet(abs_quant_metag) function works expected, and they do. Lastly, I once again defaulted all of the values in the notebooks to the standard_metag workflow.

charles-cowart commented 7 months ago

@AmandaBirmingham the issue you raised was addressed. The notebook that Charlie was running was essentially not including the synDNA columns because it's designed to default to a standard_metag workflow (which doesn't include the extra columns when tracking information associated with samples). That's why he added those columns manually right before running make_sample_sheet(). I corrected the manual additions and tested that the abs_quant workflow and the make_sample_sheet(abs_quant_metag) function works expected, and they do. Lastly, I once again defaulted all of the values in the notebooks to the standard_metag workflow.

Thanks so much Rodolfo! I'll consider this issue closed then.