Workflow: SV filtering workflow
Fetched 2023-01-10 10:36:38 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 |
|---|---|---|---|
| vcf | File | ||
| sv_intervals | https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file[] | ||
| maximum_sv_population_frequency | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| filter_sv_pop |
../tools/filter_vcf_max_sv_pop_freq.cwl
(CommandLineTool)
|
POPFREQ_AF filter | |
| interval_to_bed |
../tools/intervals_to_bed.cwl
(CommandLineTool)
|
||
| intersect_variants |
../tools/bedtools_intersect.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File[] | ||
| sv_pop_filtered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_sv_vcf.cwl
