AlexsLemonade / scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
12 stars 2 forks source link

Remove cluster metadata from SCE before merging #657

Closed sjspielman closed 9 months ago

sjspielman commented 9 months ago

Does what it says! Since we aren't keeping clusters, we should not keep the cluster parameters.

This PR was brought to you by me actually writing docs 💪 and realizing it would be super weird to document this.

sjspielman commented 9 months ago

@allyhawkins before I merge this, I might actually want to make a few small other changes I'm noticing while writing docs. What do you think of doing these?

allyhawkins commented 9 months ago

We use the metadata field merged_hvgs but the individual object is highly_variable_genes. Should we change this to be merged_highly_variable_genes for consistency?

I don't have strong feelings about this one, but the longer one is more explicit so that's fine with me.

Looks like we have named vector for library_id and sample_id. Should we unname?

This stems from how we merge the metadata using the scpcaTools function for merging SCE's. I don't think it's a big deal to keep it and I also don't think specifying named vs. unnamed is important to mention in the docs. So if we change it later we don't have to worry about maintaining that in docs.

sjspielman commented 9 months ago

Can I get another 🐈 ? https://github.com/AlexsLemonade/scpca-nf/pull/657/commits/abb2a53ce613fdf622e5d05af1bb9b31fdc20949