Workflow: adapter for sequence_align_and_tag
Fetched 2023-01-13 15:44:28 GMT
Verified with cwltool version 3.1.20221201130942
Some workflow engines won't stage files in our nested structure, so parse it out here
- 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 |
|---|---|---|---|
| reference | String |
bwa-indexed reference file |
|
| unaligned | https://w3id.org/cwl/view/git/735be84cdea041fcc8bd8cbe5728b29ca3586a21/definitions/types/sequence_data.yml#sequence_data |
the unaligned sequence data with readgroup information |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| align_and_tag |
../tools/sequence_align_and_tag.cwl
(CommandLineTool)
|
align with bwa_mem and tag |
Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| aligned_bam | File |
Permalink:
https://w3id.org/cwl/view/git/735be84cdea041fcc8bd8cbe5728b29ca3586a21/definitions/subworkflows/sequence_align_and_tag_adapter.cwl
