Workflow: pipeline.cwl
Fetched 2023-01-10 12:57:23 GMT
Verified with cwltool version 3.1.20221201130942
- 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 | ||
| overlap | Integer | ||
| block_size | Integer | ||
| nuclei_channel | String | ||
| experiment_name | String | ||
| mxif_dataset_dir_path | Directory | ||
| multichannel_ims_ometiff_negative_path | File | ||
| multichannel_ims_ometiff_positive_path | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_slicer |
steps/run_slicer.cwl
(CommandLineTool)
|
||
| run_cytokit |
steps/run_cytokit.cwl
(CommandLineTool)
|
||
| run_stitcher |
steps/run_stitcher.cwl
(CommandLineTool)
|
||
| run_combine_ims |
steps/run_combine_ims.cwl
(CommandLineTool)
|
||
| run_combine_mxif |
steps/run_combine_mxif.cwl
(CommandLineTool)
|
||
| initiate_pipeline |
steps/initiate_pipeline.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| combined_ims | File | Combined positive and negative IMS | |
| combined_mxif | File | Combined positive and negative MxIF | |
| stitched_mask | File | Stitched segmentation mask | |
| cytokit_config | File | Cytokit config | |
| pipeline_config | File | Pipeline config |
Permalink:
https://w3id.org/cwl/view/git/03b64703561d12e780d3608079f803dac0d7b5c8/pipeline.cwl
