Feature/batch adjustment - Githubissues

ebi-gene-expression-group / scxa-workflows

Higher level repo for aggregating all of Atlas workflow logic for Single Cell

Apache License 2.0

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Feature/batch adjustment #20

Closed pinin4fjords closed 4 years ago

pinin4fjords commented 4 years ago

This PR adjusts this analysis meta-repo to:

Update the Galaxy workflow to a new variant with:
- New Scanpy (v1.6.0)
- Batch adjustment with Harmony
- Object merging producing a project-level anndata file (many associated PRs to component wrappers, e.g. https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/pull/195, https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/pull/196, https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/pull/197, https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/pull/199)
Bump bundling workflow to deal with the project file (see https://github.com/ebi-gene-expression-group/scxa-bundle-workflow/pull/9)

The new Galaxy workflow can be reviewed at http://galaxy-gxa-001:8089/u/jmanning/w/scanpy-prod-160-clustering-with-harmony-batch-adjustment-h5ad.

This is paired with changes at the coordination level to deal with batches and project files: https://github.com/ebi-gene-expression-group/scxa-control-workflow/pull/25.

suhaibMo commented 4 years ago

Good work @pinin4fjords I have minor queries to understand the parameter file amendments and var declaration.

pinin4fjords commented 4 years ago

Thanks for the review @suhaibMo - will merge soon.