Workflow: pipeline.cwl
Fetched 2024-10-12 20:07:52 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
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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 |
|---|---|---|---|
| assay | String | single-cell/nucleus assay | |
| matrix | File | h5 matrix containing raw counts | |
| reference | String | Reference type to map data to | |
| secondary-analysis-matrix | File | h5 matrix to save annotations to |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| azimuth |
steps/azimuth-annotate.cwl
(CommandLineTool)
|
||
| write_metadata |
steps/write-metadata.cwl
(CommandLineTool)
|
||
| expr_h5ad_adjust |
steps/expr-h5ad-adjust.cwl
(CommandLineTool)
|
||
| extract_rna_secondary_matrix |
steps/extract-rna-secondary-matrix.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| azimuth_annotated_h5ad | File | final secondary analysis matrix with all labels and metadata |
Permalink:
https://w3id.org/cwl/view/git/f1215df5ee3c680ef18b98f1a1934874326d8d9c/pipeline.cwl
