Workflow: varscan somatic workflow
Fetched 2023-01-04 09:38:39 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 |
|---|---|---|---|
| p_value | Float (Optional) | ||
| roi_bed | File (Optional) | ||
| reference | File | ||
| tumor_bam | File | ||
| normal_bam | File | ||
| min_coverage | Integer (Optional) | ||
| min_var_freq | Float (Optional) | ||
| strand_filter | Integer (Optional) | ||
| max_normal_freq | Float (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| somatic |
../tools/varscan_somatic.cwl
(CommandLineTool)
|
varscan v2.4.2 somatic | |
| process_somatic_snvs |
../tools/varscan_process_somatic.cwl
(CommandLineTool)
|
varscan v2.4.2 processSomatic | |
| process_somatic_indels |
../tools/varscan_process_somatic.cwl
(CommandLineTool)
|
varscan v2.4.2 processSomatic |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| snvs | File | ||
| indels | File | ||
| loh_snvs | File | ||
| loh_indels | File | ||
| loh_hc_snvs | File | ||
| somatic_snvs | File | ||
| germline_snvs | File | ||
| loh_hc_indels | File | ||
| somatic_indels | File | ||
| germline_indels | File | ||
| somatic_hc_snvs | File | ||
| germline_hc_snvs | File | ||
| somatic_hc_indels | File | ||
| germline_hc_indels | File |
Permalink:
https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/subworkflows/varscan.cwl
