Workflow: starfishRunner.cwl
Fetched 2025-05-10 07:53:24 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
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- 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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| dir_size | Long (Optional) |
Size of exp_loc, in MiB. If provided, will be used to calculate ResourceRequirement. |
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| fov_count | Integer (Optional) |
The number of FOVs that are included in this experiment |
|
| 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/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/starfishRunner.cwl#decoding_blob/blob (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/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/starfishRunner.cwl#decoding_pixel/dummy (Optional) | ||
| parameter_json | File (Optional) |
JSON formatted input parameters. |
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| scatter_into_n | Integer (Optional) |
If provided, the step to run decoding will be split into n batches, where each batch is (FOV count/n) FOVs big. |
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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 |
|---|---|---|---|
| restage |
810ffa631f9a8da074dce9b0315986ab
(ExpressionTool)
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| tmpname |
tmpdir.cwl
(ExpressionTool)
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| fileDivider |
1c2f9aea647207422b1f58f502fd738c
(ExpressionTool)
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| read_schema |
371ab517ed6b5e10b21e06010b7e52bb
(CommandLineTool)
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| stage_runner |
inputParser.cwl
(ExpressionTool)
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| execute_runner |
f82ef591b72824478fa210416a90bd06
(CommandLineTool)
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| scatter_generator |
e5308895ab066382f22646f54f6e982b
(ExpressionTool)
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Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| decoded | Directory |
https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/starfishRunner.cwl
