Workflow: CODEX analysis pipeline using Cytokit
Fetched 2025-05-02 02:56:00 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
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- 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 |
|---|---|---|---|
| cytokit_config | File | ||
| cytokit_output | Directory | ||
| slicing_pipeline_config | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| second_stitching |
ometiff_second_stitching/second_stitching.cwl
(CommandLineTool)
|
||
| ome_tiff_creation |
ometiff_second_stitching/ome_tiff_creation.cwl
(CommandLineTool)
|
Create OME-TIFF versions of Cytokit segmentation and extract results |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| stitched_images | Directory | Segmentation masks and expressions in OME-TIFF format | |
| final_pipeline_config | File | Pipeline config with all the modifications |
Permalink:
https://w3id.org/cwl/view/git/cf68e50380d86410b2dc5edda79d2ef0f27314c9/steps/ometiff_second_stitching.cwl
