Workflow: Merge, annotate, and generate a TSV for SVs
Fetched 2023-01-10 17:37:02 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 |
|---|---|---|---|
| sv_vcfs | File[] | ||
| snps_vcf | File (Optional) | ||
| same_type | Boolean | ||
| cohort_name | String (Optional) | ||
| same_strand | Boolean | ||
| genome_build | String | ||
| minimum_sv_size | Integer | ||
| minimum_sv_calls | Integer | ||
| estimate_sv_distance | Boolean | ||
| max_distance_to_merge | Integer |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| merge_sv_vcfs |
../tools/survivor.cwl
(CommandLineTool)
|
Run SURVIVOR to merge SV calls | |
| annotate_variants |
../tools/annotsv.cwl
(CommandLineTool)
|
||
| bgzip_merged_sv_vcf |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| merged_sv_vcf | File | ||
| merged_annotated_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/e56f1024306aeb427d8aae2fff715ed2e8b8f86f/definitions/subworkflows/merge_svs.cwl
