Workflow: pipeline.cwl
Fetched 2025-04-29 10:01:15 GMT
Verified with cwltool version 3.1.20230201224320
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- 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 | ||
| data_dir | Directory | ||
| meta_path | File | ||
| segmentation_method | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| collect_output |
steps/collect_output.cwl
(CommandLineTool)
|
Collect segmentation masks and images for the final output | |
| run_segmentation |
steps/run_segmentation.cwl
(CommandLineTool)
|
Run segmentation | |
| collect_dataset_info |
steps/collect_dataset_info.cwl
(CommandLineTool)
|
Collect dataset info | |
| prepare_segmentation_channels |
steps/prepare_segmentation_channels.cwl
(CommandLineTool)
|
Prepare images for segmentation |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| pipeline_output | Directory | Expressions and segmentation masks in OME-TIFF format |
Permalink:
https://w3id.org/cwl/view/git/cd2f15fe021a727cf92a96e5b156f846d38e0daa/pipeline.cwl
