Comments (4)
I'm going to suggest that the main functions for generating this report should live in https://github.com/AlexsLemonade/scpcaTools Then we can build that package into the scpca-r docker image and generate the QC reports with a pretty minimal workflow.
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Yes agreed. There is an issue in scpcaTools for generating the function(s) that will actually be used to generate the QC report as well. Including that here for reference: AlexsLemonade/scpcaTools#7
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Noting that this will happen in the new https://github.com/AlexsLemonade/scpca-nf repo.
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Functionally blocked by updates to scpcaTools to support taking two SCE objects.
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Related Issues (20)
- Discussion: Should we change the merged publish directory to be the given project directory? HOT 4
- Specify run ids to use when merging projects HOT 1
- Add sentence to cell type report indicating references come from normal samples HOT 2
- [BUG] CellAssign process getting killed with `OutOfMemoryError` HOT 10
- Ideas for reducing file sizes HOT 6
- Add is_xenograft & is_cell_line to example metadata HOT 6
- 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`
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