Comments (3)
Images for single-tool containers have been added, but something more advanced is needed for more complex Python (and R) environments.
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Temporary Docker images have been created in #17 for the more complex environments, but we should check if there is a more optimal solution.
from spatialvi.
One possibility is to actually create a mulled container for processes (multi container) via bioconda for these. Then you do not need to build and host your own. This is entirely possible with your current setup, as the recipes are already used anyways :-)
from spatialvi.
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 12
- 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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