Workflow: SPRM pipeline
Fetched 2025-03-02 14:28:10 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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) | |
| 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) | |
| cell_types_file | File (Optional) | Cell type annotations file | |
| enable_faulthandler | Boolean (Optional) | Whether to enable the Python 'faulthandler' module |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sprm |
steps/sprm.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 |
Permalink:
https://w3id.org/cwl/view/git/d2d5127251fbec9f9621df0c6c8c989e3f1b76ba/pipeline.cwl
