Workflow: CODEX analysis pipeline using Cytokit
Fetched 2025-11-11 13:36:18 GMT
Verified with cwltool version 3.1.20221201130942
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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 |
|---|---|---|---|
| run_cytokit |
steps/run_cytokit.cwl
(CommandLineTool)
|
||
| ometiff_second_stitching |
steps/ometiff_second_stitching.cwl
(Workflow)
|
CODEX analysis pipeline using Cytokit | |
| illumination_first_stitching |
steps/illumination_first_stitching.cwl
(Workflow)
|
CODEX analysis pipeline using Cytokit |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| data_json | File | JSON file containing Cytokit's calculations from deconvolution, drift compensation, and focal plane 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/d8efe116c9fd79d21646ec215799b52b95dfd709/pipeline.cwl
