Workflow: qc.cwl

Fetched 2024-06-10 10:40:09 GMT
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Inputs

ID Type Title Doc
roi File (Optional)

The location of the RoiSet.zip, if applicable.

data https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/qc.cwl#data/pkl (Optional)
codebook https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/qc.cwl#codebook/exp (Optional)
data_exp Directory (Optional)

Flattened data input, refer to record entry.

save_pdf Boolean (Optional)

If true, will save graphical output to a pdf.

has_spots Boolean (Optional)

If true, will look for spots within the experiment field.

imagesize https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/qc.cwl#imagesize/locs (Optional)
locs_json File (Optional)

Flattened json input, refer to record entry.

find_ripley Boolean (Optional)

If true, will run ripley K estimates to find spatial density measures. Can be slow.

codebook_exp Directory (Optional)

Flattened codebook input, refer to record entry.

codebook_pkl File (Optional)

Flattened codebook input, refer to record entry.

selected_fovs Integer[] (Optional)

If provided, QC will only be run on FOVs with these indices.

data_pkl_spots File (Optional)

Flattened data input, refer to record entry.

parameter_json File (Optional)

The json with parameters to be read in for the following variables.

spot_threshold Float (Optional)

If has_spots is true and this is provided, spots with an intensity lower than this will not be included in qc metrics

segmentation_loc Directory (Optional)

The location of the output from the segmentation step, if it was performed.

data_pkl_transcripts File (Optional)

Flattened data input, refer to record entry.

Steps

ID Runs Label Doc
tmpname
tmpdir.cwl (ExpressionTool)
stage_qc
inputParser.cwl (ExpressionTool)
execute_qc
575065a1a692cadbd0eba3c4a73467cd (CommandLineTool)
read_schema
d2ebe601fcde5da95eccf56733dbff96 (CommandLineTool)
codebook_grabber
a3aae3263a9332280c4a6b87007dd0ad (ExpressionTool)

Outputs

ID Type Label Doc
qc_metrics Directory
Permalink: https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/qc.cwl