Workflow: HS Metrics workflow
Fetched 2023-01-11 12:10:27 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| bam | File | ||
| reference | File | ||
| summary_intervals | https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_mapping_quality | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| collect_summary_hs_metrics |
../tools/collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics | |
| collect_per_base_hs_metrics |
../tools/collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics | |
| collect_per_target_hs_metrics |
../tools/collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| summary_hs_metrics | File[] | ||
| per_base_hs_metrics | File[] | ||
| per_target_hs_metrics | File[] | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/subworkflows/hs_metrics.cwl
