Workflow: adapter for sequence_align_and_tag
Fetched 2023-01-04 18:39:25 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
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| trimming | https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| reference | File |
bwa-indexed reference file |
|
| unaligned | https://w3id.org/cwl/view/git/336f7d1af649f42543baa6be2594cd872919b5b5/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/336f7d1af649f42543baa6be2594cd872919b5b5/definitions/subworkflows/sequence_align_and_tag_adapter.cwl
