Workflow: haplotypecaller.cwl
Fetched 2023-01-12 15:27:25 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| snp_ref | File | ||
| bam_file | File | ||
| interval | File | ||
| job_uuid | String | ||
| reference | File | ||
| sample_name | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| picard_sortvcf |
../../tools/variant_calling/picard_sortvcf.cwl
(CommandLineTool)
|
||
| gatk3_haplotypecaller |
../../tools/variant_calling/gatk3_haplotypercaller.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| haplotypecaller_sorted_vcf | File | ||
| time_metrics_from_picard_sortvcf | File | ||
| time_metrics_from_gatk3_haplotypecaller | File |
Permalink:
https://w3id.org/cwl/view/git/f55f0011de7db66f873ffb0f700f3fe26b33911e/genomel/cwl/workflows/variant_calling/haplotypecaller.cwl
