Workflow: starfishRunner.cwl

Fetched 2023-03-15 15:46:32 GMT
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Inputs

ID Type Title Doc
exp_loc Directory

Location of directory containing starfish experiment.json file

rescale Boolean (Optional)

Whether to iteratively rescale images before running the decoder.

is_volume Boolean (Optional)

Whether to treat the zplanes as a 3D image.

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.

use_ref_img Boolean (Optional)

Whether to generate a reference image and use it alongside spot detection.

level_method String (Optional)

Levelling method for clip and scale application. Defaults to SCALE_BY_IMAGE.

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.

decoding_pixel https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/starfishRunner.cwl#decoding_pixel/dummy (Optional)
parameter_json File (Optional)

JSON formatted input parameters.

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
read_schema
12bb80496e6ad51754f7793abe126f5a (CommandLineTool)
stage_runner
inputParser.cwl (ExpressionTool)
execute_runner
df9cc30b21d18efe7b5f89a6af64745a (CommandLineTool)

Outputs

ID Type Label Doc
decoded Directory
Permalink: https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/steps/starfishRunner.cwl