Workflow: scatter-gatk-wf-with-interval.cwl
Fetched 2023-01-04 01:17:52 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
GNU Affero General Public License v3.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| sample | String | ||
| reference | File | ||
| knownsites1 | File | ||
| scattercount | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| merge-GVCFs |
gather-array-vcf.cwl
(CommandLineTool)
|
Gathering vcf using Picard | |
| splitintervals |
gatk-splitintervals.cwl
(CommandLineTool)
|
Creating interval files for scattering | |
| recal-haplotypecaller |
gatk-wf-with-interval.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatheredgvcf | File |
Permalink:
https://w3id.org/cwl/view/git/b50ffeeeae865d0780ca03c5a3f5065eeeb758e4/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
