Workflow: SPRM pipeline
Fetched 2026-10-11 12:08:57 GMT
Verified with cwltool version 3.1.20230201224320
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- Default Values
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU General Public License v3.0 only
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| verbose | Boolean (Optional) | Whether to enable verbose/debug mode | |
| mask_dir | Directory | Directory containing mask files | |
| image_dir | Directory | Directory containing image files | |
| processes | Integer (Optional) | Number of images to process in parallel (default: 1) | |
| min_memory | Boolean (Optional) | Whether to conserve memory by leaving large arrays on disk | |
| options_file | File (Optional) | SPRM options file | |
| enable_manhole | Boolean (Optional) | Whether to enable remote debugging via 'manhole' | |
| options_preset | String (Optional) | SPRM options preset (alternate options file bundled with the package) | |
| threadpool_limit | Integer (Optional) | Whether to enable the Python 'faulthandler' module | |
| enable_faulthandler | Boolean (Optional) | Whether to enable the Python 'faulthandler' module | |
| cell_types_directory | Directory[] (Optional) | Cell type annotations file |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sprm |
steps/sprm.cwl
(CommandLineTool)
|
SPRM analysis | |
| create_spatial_data |
steps/create-spatial-data.cwl
(CommandLineTool)
|
SPRM analysis | |
| ome_tiff_normalize_expr |
ome-tiff-normalize/ome_tiff_normalize.cwl
(CommandLineTool)
|
OME-TIFF metadata normalization via bftools | |
| ome_tiff_normalize_mask |
ome-tiff-normalize/ome_tiff_normalize.cwl
(CommandLineTool)
|
OME-TIFF metadata normalization via bftools |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sprm_output | Directory | SPRM output | |
| sdata_zarr_zips | File[] | ||
| segmentation_metadata_json | File |
Permalink:
https://w3id.org/cwl/view/git/002cd44249383171312b6df85cebc247e87b606d/pipeline.cwl
