Workflow: Detect DoCM variants
Fetched 2023-01-11 00:29:35 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 |
|---|---|---|---|
| cram | File | ||
| docm_vcf | File | ||
| reference | String | ||
| interval_list | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bgzip |
../detect_variants/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index |
../detect_variants/index.cwl
(CommandLineTool)
|
vcf index | |
| docm_filter |
single_sample_docm_filter.cwl
(CommandLineTool)
|
docm filter | |
| gatk_haplotypecaller |
germline_gatk_haplotypecaller.cwl
(CommandLineTool)
|
HaplotypeCaller (GATK 3.6) |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File | ||
| unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/ab3cc1f460146c60d7de417508f0c1ea70506e6a/docm/germline_workflow.cwl
