Workflow: CODEX analysis pipeline using Cytokit
Fetched 2023-01-10 13:05:51 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- Default Values
- Nested Workflows
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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 |
|---|---|---|---|
| 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 |
|---|---|---|---|
| slicing |
steps/slicing.cwl
(CommandLineTool)
|
||
| best_focus |
steps/best_focus.cwl
(CommandLineTool)
|
||
| run_cytokit |
steps/run_cytokit.cwl
(CommandLineTool)
|
||
| first_stitching |
steps/first_stitching.cwl
(CommandLineTool)
|
||
| second_stitching |
steps/second_stitching.cwl
(CommandLineTool)
|
||
| ome_tiff_creation |
steps/ome_tiff_creation.cwl
(CommandLineTool)
|
Create OME-TIFF versions of Cytokit segmentation and extract results | |
| 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 | |
| background_subtraction |
steps/background_subtraction.cwl
(CommandLineTool)
|
||
| illumination_correction |
steps/illumination_correction.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| data_json | File | JSON file containing Cytokit's calculations from deconvolution, drift compensation, and focal plan selection | |
| pipeline_config | File | Pipeline config with all the modifications | |
| stitched_images | Directory | Segmentation masks and expressions in OME-TIFF format | |
| experiment_config | File | Cytokit configuration format |
Permalink:
https://w3id.org/cwl/view/git/2fc3446c56128a7b13eb451e755cad8937b979ba/pipeline.cwl
