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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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need well_id_96 information added to metagenomics samplesheets #122

Closed mmbryant23 closed 9 months ago

mmbryant23 commented 1 year ago

Currently well_id_96 information is not being exported into NovaSeq samplesheets and therefore not being carried over into the preparation file for the sequencing run. The steps to do this are as follows: 1) well_id_96 information column is inputed into the notebook via the 384-well compressed gDNA plate map (this is complete) 2) well_id_96 information column needs to be exported into the NovaSeq samplesheet information via the metagenomics pooling notebook (this is needed) 3) well_id_96 information column is carried over from the samplesheet into the preparation file generated by the SPP (i believe this has been completed for MiSeq amplicon pre-preparation files, but there may be additional changes needed for this to happen with NovaSeq samplesheets)

mmbryant23 commented 1 year ago

After well_id_96 is successfully added, I believe we should changing the naming of "well_id" in the amplicon pre-preparation file to "well_id_384", and "Sample_Well" in the NovaSeq samplesheet to "well_id"384". This will specify in what plate the wells are being referred to, standardize naming format, and introduce consistency between amplicon and shotgun column names.

This change will likely affect the notebooks and likely SPP for amplicon and shotgun.

charles-cowart commented 1 year ago

After well_id_96 is successfully added, I believe we should changing the naming of "well_id" in the amplicon pre-preparation file to "well_id_384", and "Sample_Well" in the NovaSeq samplesheet to "well_id"384". This will specify in what plate the wells are being referred to, standardize naming format, and introduce consistency between amplicon and shotgun column names.

This change will likely affect the notebooks and likely SPP for amplicon and shotgun.

Hi @mmbryant23! Just to clarify, both well_id and Sample_Well are going to be changed to well_id_384? Or does Sample_Well need to be changed into something else instead?

mmbryant23 commented 1 year ago

Yes, both well_id (pre-preparation file for amplicon) and Sample Well (samplesheet for metagenomics) are going to be changed to well_id_384. This will introduce standardized naming between well_id formats (96 vs 384) and harmonize the naming between amplicon + metaG/T. Thanks for checking!

On Mon, Jul 17, 2023 at 5:19 PM Charles Cowart @.***> wrote:

After well_id_96 is successfully added, I believe we should changing the naming of "well_id" in the amplicon pre-preparation file to "well_id_384", and "Sample_Well" in the NovaSeq samplesheet to "well_id"384". This will specify in what plate the wells are being referred to, standardize naming format, and introduce consistency between amplicon and shotgun column names.

This change will likely affect the notebooks and likely SPP for amplicon and shotgun.

Hi @mmbryant23 https://github.com/mmbryant23! Just to clarify, both well_id and Sample_Well are going to be changed to well_id_384? Or does Sample_Well need to be changed into something else instead?

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/issues/122#issuecomment-1638897357, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVY3ITRNDDSLO62QEJQWU5LXQWT4PANCNFSM6AAAAAAXTA56C4 . You are receiving this because you were mentioned.Message ID: @.***>

charles-cowart commented 1 year ago

Yes, both well_id (pre-preparation file for amplicon) and Sample Well (samplesheet for metagenomics) are going to be changed to well_id_384. This will introduce standardized naming between well_id formats (96 vs 384) and harmonize the naming between amplicon + metaG/T. Thanks for checking! …

Wonderful! Thanks for confirming!

charles-cowart commented 1 year ago

@mmbryant23 I apologize but could you restate the issue in terms of specific notebooks? I'm a little confused. Perhaps we can schedule a Zoom to walk through this issue together? Thanks!

mmbryant23 commented 1 year ago

Sure thing - I'm available at 11am if you want to chat - Can you please send over the zoom link via email? Thanks!

On Wed, Aug 2, 2023 at 1:38 PM Charles Cowart @.***> wrote:

@mmbryant23 https://github.com/mmbryant23 I apologize but could you restate the issue in terms of specific notebooks? I'm a little confused. Perhaps we can schedule a Zoom to walk through this issue together? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/issues/122#issuecomment-1662677104, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVY3ITQ5URC2DQDHUM56L3LXTKGADANCNFSM6AAAAAAXTA56C4 . You are receiving this because you were mentioned.Message ID: @.***>

charles-cowart commented 1 year ago

Addressed by https://github.com/biocore/metagenomics_pooling_notebook/pull/138, later https://github.com/biocore/metagenomics_pooling_notebook/pull/139