Workflow: find_hotspots_in_normals.cwl
Fetched 2024-05-04 20:22:27 GMT
Verified with cwltool version 3.1.20230201224320
Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
| sample_ids | String[] | ||
| patient_ids | String[] | ||
| hotspot_list | File | ||
| duplex_pileups | File[] | ||
| sample_classes | String[] | ||
| unfiltered_pileups | File[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| find_hotspots_in_normals |
../../cwl_tools/bioinfo_utils/find_hotspots_in_normals.cwl
(CommandLineTool)
|
||
| plot_hotspots_in_normals |
../../cwl_tools/bioinfo_utils/plot_hotspots_in_normals.cwl
(CommandLineTool)
|
||
| print_hotspots_in_normals_table |
../../cwl_tools/bioinfo_utils/print_hotspots_in_normals_table.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| hotspots_in_normals_data | File | ||
| hotspots_in_normals_plot | File | ||
| hotspots_in_normals_table_pdf | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/subworkflows/find_hotspots_in_normals.cwl
