Workflow: qc.cwl
Fetched 2024-11-25 04:56:30 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
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 |
cac532eb674987739749ca9d554b4923
(CommandLineTool)
|
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| read_schema |
79e5c073b509c718838371718bd7e839
(CommandLineTool)
|
||
| codebook_grabber |
ab659f8f82c7ac56c79aaa5e64c1e39c
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qc_metrics | Directory |
https://w3id.org/cwl/view/git/2e31b8ddd4d509c7bbcb983ad41e401687623ddb/steps/qc.cwl
