Update consensus cell type module to output one file for each library

[allyhawkins]

Closes #114

Here I'm porting over the changes made in AlexsLemonade/OpenScPCA-analysis#1010 to output consensus cell types for each library in a separate TSV file. I copied over the script that is in OpenScPCA-analysis repo and made the appropriate changes to the workflow to have just the single process for assigning labels. I also added the blueprint reference as a parameter and updated the link for the consensus reference since that was slightly modified.

I ran this using the testing profile locally (thanks for setting that up!) and it completed successfully. I'll do a full testing run with simulated data once I file this PR and will request review once that run completes.

[jashapiro]

This looks good from a first glance, but I wonder if we want to wait for the point release of openscpca-analysis to put this in so we can add in the versioned docker image? It might make it easier to reference the reference files as well (more human-readable, anyway).

[allyhawkins]

This looks good from a first glance, but I wonder if we want to wait for the point release of openscpca-analysis to put this in so we can add in the versioned docker image? It might make it easier to reference the reference files as well (more human-readable, anyway).

Yes I was just starting to work on getting things done for the release, so that is my plan.

[allyhawkins]

Noting that the test run worked successfully, but I want to wait to get this in after we do a release of OpenScPCA-analysis which is dependent on fixing the failed workflow run. So putting this on hold temporarily.

[allyhawkins]

@jashapiro I updated this to use the versioned image. I'm running a test run now, but this should be ready for a formal review.

[jashapiro]

This looks good to me. The main change that I suggested is using the git tag for the reference files, as I think it will be easier to see if it is up to date as needed.

Other than that (and a minor formatting suggestions), I think this should be good to go.

[jashapiro]

Do we want to update all modules? Seems like we might want to, but we could do that in a separate PR

[allyhawkins]

Noting that I made the changes you suggested and test run completed successfully, so going to go ahead and merge this.