Workflow: qc.cwl
Fetched 2023-09-02 22:52:50 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/e7f46046a7338b6a2bb914e263278ea9c0207326/steps/qc.cwl#data/pkl (Optional) | ||
| codebook | https://w3id.org/cwl/view/git/e7f46046a7338b6a2bb914e263278ea9c0207326/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/e7f46046a7338b6a2bb914e263278ea9c0207326/steps/qc.cwl#imagesize/fov_positioning (Optional) | ||
| 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 |
8fa782e4291c0494d07cff90c199072b
(CommandLineTool)
|
||
| read_schema |
6a6859d2bc5432895fcb70c28e92c946
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qc_metrics | Directory |
https://w3id.org/cwl/view/git/e7f46046a7338b6a2bb914e263278ea9c0207326/steps/qc.cwl
