- 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 |
---|---|---|---|
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