Workflow: CODEX analysis pipeline using Cytokit
Fetched 2023-01-04 01:13:40 GMT
Verified with cwltool version 3.1.20221201130942
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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 |
|---|---|---|---|
| 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/a04e55b0fd73afbed8d29b2040dd9c438ba666a6/pipeline.cwl
