Workflow: CODEX analysis pipeline using Cytokit
Fetched 2024-05-04 13:25:11 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 |
|---|---|---|---|
| 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 | |
| background_subtraction |
ometiff_second_stitching/background_subtraction.cwl
(CommandLineTool)
|
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/16794b6359ae24a83226a583c527418ac3d3424f/steps/ometiff_second_stitching.cwl
