Workflow: CODEX analysis pipeline using Cytokit
Fetched 2025-11-02 05:48:57 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| gpus | String | GPUs to use, represented as a comma-separated list of integers. | |
| data_dir | Directory | Directory containing CODEX data |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_sprm |
steps/run_sprm.cwl
(CommandLineTool)
|
Run Spatial Process & Relationship Modeling (SPRM) | |
| cytokit_operator |
steps/cytokit_operator.cwl
(CommandLineTool)
|
CODEX analysis via Cytokit | |
| cytokit_processor |
steps/cytokit_processor.cwl
(CommandLineTool)
|
CODEX analysis via Cytokit | |
| ome_tiff_creation |
steps/ome_tiff_creation.cwl
(CommandLineTool)
|
Create OME-TIFF versions of Cytokit segmentation and extract results | |
| create_dir_for_viz |
steps/create_dir_for_viz.cwl
(CommandLineTool)
|
Create directory containing symlinks to relevant files for visualization team | |
| create_yaml_config |
steps/create_yaml_config.cwl
(CommandLineTool)
|
Create Cytokit experiment config | |
| collect_dataset_info |
steps/collect_dataset_info.cwl
(CommandLineTool)
|
Collect dataset info for Cytokit |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| data_json | File | JSON file containing Cytokit's calculations from deconvolution, drift compensation, and focal plan selection | |
| for_viz_dir | File | Archive of symbolic links to files for visualization team | |
| ome_tiff_output | Directory | Segmentation masks in OME-TIFF format | |
| sprm_output_dir | Directory | Directory containing all SPRM outputs | |
| experiment_config | File | Cytokit configuration format |
Permalink:
https://w3id.org/cwl/view/git/221f7c4215e926f3e816bac60812007601d45e5d/pipeline.cwl
