Related Issues (20)
- Create outputs readable by e.g. TissUUmaps, Loupe
- Module compilation error - cause: unable to resolve class JsonSlurper HOT 2
- Module compilation error HOT 2
- Add documentation for "Analysis options" in `usage.md` HOT 1
- Is Space Ranger Cytassist supported? HOT 2
- Implement tests using nf-test HOT 1
- Update spaceranger to 2.x HOT 8
- It should be possible to provide manual image alignments on a per-sample basis
- Add SpatialData as output HOT 20
- Add MultiQC report HOT 13
- Add checks for QC filtering HOT 2
- Auto-detection of samplesheet type HOT 1
- Full-size test dataset
- Version exporting of `leidenalg` and `SpatialDE` does not work
- Aggregate samples into single object HOT 4
- Rename the pipeline HOT 1
- Missing SpatialDE package in Docker container for ST_SPATIAL_DE process HOT 3
- Use `to_legacy_anndata` function from `spatialdata_io` instead of custom code HOT 1
- Option to use the `--unknown-slide` parameter in `spaceranger count` HOT 1
- MultiQC 1.21 doesn't support genomic_dna section HOT 1
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