Workflow: Pipeline for converting dcc files output by GeoMX into sample by gene matrices
Fetched 2026-08-11 06:37:38 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| data_directory | Directory | Path to directory containing dcc files and pkc file | |
| enable_manhole | Boolean (Optional) | Whether to enable remote debugging via 'manhole' |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| make-sample-by-gene |
steps/make-sample-by-gene.cwl
(CommandLineTool)
|
Converts vendor output to H5AD | |
| adjust-ometiff-channels |
steps/adjust-ometiff-channels.cwl
(CommandLineTool)
|
Replaces channels in OME-TIFF metadata |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| h5ad_file | File | ||
| ome_tiff_directory | Directory |
Permalink:
https://w3id.org/cwl/view/git/25f3f48afd4901fdf73ceeb6a3e02f7744ba7619/pipeline.cwl
