Upload raw data from 10X experiment and visualize it

Upload raw data from 10X experiment and visualize it

Carl would like to upload their raw sequence data from an experiment, combined with other BICCN data, and use the BICCN analysis pipeline (Optimus pipeline) to analyze the data, assign default clusters and visualize this data. This would entail the following steps:

1. Carl first uploads raw 10X data to NeMO Archive (fastq files).
2. After upload, he searches for data of interest using the NeMO Faceted Search.
3. After he finds the data he adds it to a cart and then transfers the data to Terra (using hand-off UI).
4. Once in Terra he uses the data model to run the Optimus pipeline to get expression matrices.
5. After Optimus competes, he runs the Cumulus pipeline to generate embedding, de novo clusters, and differential expression.
6. Once Cumulus completes he goes to the Single Cell Portal (SCP) and makes a study based on the existing workspace.
7. He moves files into the SCP using the "Sync Files" UI.
8. The portal parses and visualizes the data.
9. Carl now visualizes metadata and gene expression in the embedding.
10. Happy, Carl shares the study with collaborators and eventually makes the study public.
    (Thoughts on circling back to NeMO are welcome).