Workflow: varscan somatic workflow
Fetched 2024-11-25 04:42:29 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
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/656d9ae18f164f983c5672bcf51037cd73309f4f/subworkflows/varscan.cwl
