- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
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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. |
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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/03b8da4ede3afcbf97b4e780c153155f33e76c84/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/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/starfishRunner.cwl#decoding_pixel/dummy (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 |
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read_schema |
12bb80496e6ad51754f7793abe126f5a
(CommandLineTool)
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stage_runner |
inputParser.cwl
(ExpressionTool)
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execute_runner |
df9cc30b21d18efe7b5f89a6af64745a
(CommandLineTool)
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Outputs
ID | Type | Label | Doc |
---|---|---|---|
decoded | Directory |
https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/starfishRunner.cwl