Workflow: CODEX analysis pipeline using Cytokit
Fetched 2025-01-22 19:10:34 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 |
|---|---|---|---|
| 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 |
illumination_first_stitching/slicing.cwl
(CommandLineTool)
|
||
| best_focus |
illumination_first_stitching/best_focus.cwl
(CommandLineTool)
|
||
| first_stitching |
illumination_first_stitching/first_stitching.cwl
(CommandLineTool)
|
||
| create_yaml_config |
illumination_first_stitching/create_yaml_config.cwl
(CommandLineTool)
|
Create Cytokit experiment config | |
| collect_dataset_info |
illumination_first_stitching/collect_dataset_info.cwl
(CommandLineTool)
|
Collect dataset info for Cytokit | |
| illumination_correction |
illumination_first_stitching/illumination_correction.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| new_tiles | Directory | ||
| cytokit_config | File | Cytokit configuration in YAML format | |
| slicing_pipeline_config | File | Pipeline config with all the modifications |
Permalink:
https://w3id.org/cwl/view/git/1c7394266f64fdf88a67d8a6507644543f489c17/steps/illumination_first_stitching.cwl
