Workflow: gatk3_realignment.cwl
Fetched 2023-01-12 03:38:00 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 |
|---|---|---|---|
| bam_path | File | ||
| job_uuid | String | ||
| reference | File | ||
| known_indel1 | File | ||
| known_indel2 | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gatk3_indelrealigner |
../../tools/realignment/gatk3_indelrealigner.cwl
(CommandLineTool)
|
||
| gatk3_leftalignindels |
../../tools/realignment/gatk3_leftalignindels.cwl
(CommandLineTool)
|
||
| gatk3_realignertargetcreator |
../../tools/realignment/gatk3_realignertargetcreator.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| harmonized_realigned_bam | File | ||
| time_metrics_from_gatk3_indelrealigner | File | ||
| time_metrics_from_gatk3_leftalignindels | File | ||
| time_metrics_from_gatk3_realignertargetcreator | File |
Permalink:
https://w3id.org/cwl/view/git/1595f2bc453663c9e71c1a2d60729f481921029e/genomel/cwl/workflows/realignment/gatk3_realignment.cwl
