Workflow: Detect DoCM variants
Fetched 2023-05-12 16:14:55 GMT
Verified with cwltool version 3.1.20230201224320
- 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 |
|---|---|---|---|
| bam | File | ||
| docm_vcf | File | ||
| reference | String | ||
| interval_list | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| docm_filter |
../tools/single_sample_docm_filter.cwl
(CommandLineTool)
|
docm filter | |
| gatk_haplotypecaller |
../tools/docm_gatk_haplotype_caller.cwl
(CommandLineTool)
|
HaplotypeCaller (GATK 3.6) |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| filtered_vcf | File | ||
| unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/72e0bdc1ec449d86df4534132e9a30ad7e9b8afd/definitions/subworkflows/docm_germline.cwl
