Workflow: starfishRunner.cwl
Fetched 2026-10-01 14:40:56 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| exp_loc | Directory |
Location of directory containing starfish experiment.json file |
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| rescale | Boolean (Optional) |
Whether to iteratively rescale images before running the decoder. |
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| is_volume | Boolean (Optional) |
Whether to treat the zplanes as a 3D image. |
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| anchor_view | String (Optional) |
The name of the auxillary view to be used as a reference view, such as for anchor round in ISS processing. Will not be included if not provided. |
|
| n_processes | Integer (Optional) |
If provided, the number of processes that will be spawned for processing. Otherwise, the maximum number of available CPUs will be used. |
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| use_ref_img | Boolean (Optional) |
Whether to generate a reference image and use it alongside spot detection. |
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| level_method | String (Optional) |
Levelling method for clip and scale application. Defaults to SCALE_BY_IMAGE. |
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| decoding_blob | https://w3id.org/cwl/view/git/6ef7a6399b2ab55c1d3edd4e37631a8234889fd9/steps/starfishRunner.cwl#decoding_blob/dummy (Optional) | ||
| selected_fovs | Integer[] (Optional) |
If provided, starfish will only be run on FOVs with these indices. |
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| decoding_pixel | https://w3id.org/cwl/view/git/6ef7a6399b2ab55c1d3edd4e37631a8234889fd9/steps/starfishRunner.cwl#decoding_pixel/pixel (Optional) | ||
| parameter_json | File (Optional) |
JSON formatted input parameters. |
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| not_filtered_results | Boolean (Optional) |
Will not remove genes that do not match a target and do not meet criteria. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tmpname |
tmpdir.cwl
(ExpressionTool)
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| read_schema |
8ddc1fbbc8f633f0ebbebe563ef008dd
(CommandLineTool)
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| stage_runner |
inputParser.cwl
(ExpressionTool)
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| execute_runner |
d898bc51d84f3b5894dca868d34b34fe
(CommandLineTool)
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Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| decoded | Directory |
https://w3id.org/cwl/view/git/6ef7a6399b2ab55c1d3edd4e37631a8234889fd9/steps/starfishRunner.cwl
