biocore / metagenomics_pooling_notebook / 11733684595
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Multiproject plate support, updated blanks handling (#248)

* Brings up to date with current master (#218)

* Fixed demuxed sample-sheet generation (#215)

* Fixed demuxed sample-sheet generation

Demuxed sample-sheets now use orig_name for their sample-name column
values, instead of the sample_name column.

* Cleanup

* Dev metaT notebook (#207)

* Minor changes for new sequencer support and RNA quant. Added metatrasncrptomics notebook.

Made changes to the available sequencer platforms and their associated i5 index orientation. Changed max_concentration for quants to allow for wider range of observed values for RNA quant. Added metatranscritpmics notebook and associated test_data.

* Added compatibility for prep_files for sample sequence count merge.

also fixed some flake8

* added tests for sequence count merge from prep-file

* updated available sequencing platforms to include NovaSeqX and NovaSeqXPlus

Renamed NovaSeq to NovaSeq6000. Addresses #176

* changed default normalization_column to 'Raw Reads'

* Addressed Pull Request review comments.

Added requested descriptions and clarifications. Modified the text introduction in the matrix tube pipeline to better reflect the new matrix tube specific methodology.

* Fixed small typos and added extra clarifications

* Updates to satisfy the linter

---------

Co-authored-by: Charles Cowart <42684307+charles-cowart@users.noreply.github.com>
Co-authored-by: Charles Cowart <ccowart@ucsd.edu> (Just some linting stuff and merge conflict resolution nothing big)

---------

Co-authored-by: Charles Cowart <42684307+charles-cowart@users.noreply.github.com>
Co-authored-by: RodolfoSalido <rodolfo.salido@gmail.com>

* Sample sheet support for new SampleContext section (#219)

* typo clean-ups and a mutable default fix

* add new sample sheet type with SampleContext section to list blank info; generalized handling of "extra" df sections in KLSampleSheet

* cod... (continued)

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