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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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metagenomics_pooling_notebook: Well_description in novaseq samplesheet should have the same format as well_description in the amplicon pre-preparation file #120

Closed mmbryant23 closed 1 year ago

mmbryant23 commented 1 year ago

Currently the Well_description column in a NovaSeq samplesheet contains only the sample name formatted in a Qiita-friendly manner. This is not useful and it would be beneficial if the format of the Well_description in the Novaseq samplesheet to contain the same information as the well_description in the amplicon pre-preparation file. I think this should affect both metagenomics pooling notebooks being used to generate sample sheets (metagenomics_pipeline_MiniPiconorm.ipynb and metagenomics_pipeline_iSeqnorm.ipynb)

Current amplicon pre-preparation file format: (project_name).(project_plate).(well_id) Example: ABTX_11052_Plate_191.8.18.20.RK.ST.1315.A1

Current NovaSeq samplesheet format: (Sample_Name) Proposed NovaSeq samplesheet format: (Sample_Plate).(Sample_Name).(Sample_Well)

Example: Current:

Screen Shot 2023-04-28 at 4 52 31 PM

Proposed:

Screen Shot 2023-04-28 at 4 53 43 PM

Additional information from Rodolfo regarding the code in the metagenomics pooling notebook:

Screen Shot 2023-04-28 at 4 07 24 PM
charles-cowart commented 1 year ago

Confirmed the code in amplicon_pre_prep_file_generator notebook uses the generate_qiita_prep_file() in metapool to generate well_descriptions of the form sample_plate' + 'sample_name' + 'well_id' columns.

charles-cowart commented 1 year ago

Addressed in https://github.com/biocore/metagenomics_pooling_notebook/pull/137