Comments (2)
From our discussion in DSTM today we have decided to keep separate AnnData
objects for CITE-seq and RNA data. This means we are going to have 2 files for every library that contains ADT or hashing data - 1 for the ADT/hashing object and the other for RNA.
We may still want to use muData
to store the two AnnData objects for easier processing through Nextflow, but the final output should be two separate files.
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Closed by #355
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Related Issues (20)
- Create nextflow_schema.json file HOT 1
- Include instructions for specifying `merge_run_ids` when merging projects in external instructions
- Skip creation of merged objects HOT 1
- Fix column name typos HOT 4
- Future idea: Create merged objects for projects with multiplexed libraries containing all non-multiplexed single-cell libraries
- Prepare for scpca-nf release v0.7.3
- Make sure CellAssign is skipped for any objects with just 1 cell HOT 1
- [BUG] Age in sample_metadata is inconsistently typed HOT 3
- Discussion: Rename AnnData objects with .h5ad extension HOT 6
- [BUG] Account for grabbing estimated demux cell counts for libraries with no genetic demultiplexing HOT 1
- `project_celltype_metafile` parameter is missing from scpca-nf schema
- Test workflow with Bioc3.19 images HOT 1
- Use more specialized docker images for processes HOT 2
- Prepare for scpca-nf release `v0.8.1`
- Consider using nf-schema plugin to validate inputs
- Use new smaller images in processes HOT 1
- Test use of smaller Docker images in workflow HOT 1
- Re-order bulk metadata to match order for overall sample metadata HOT 1
- Add sample metadata table to QC and cell type reports HOT 5
- Output bulk data to a `bulk` folder rather than individual files within project directory HOT 1
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