- 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 | File | ||
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 (GATK4) |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
filtered_vcf | File | ||
unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/subworkflows/docm_germline.cwl