- 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 | String | ||
tumor_cram | File | ||
normal_cram | 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/891c996dbd23d8154ec7609a56da3de841ae124c/definitions/subworkflows/varscan.cwl