Workflow: downsample unaligned BAM and align
Fetched 2023-01-11 09:21:27 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:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| mills | File | ||
| dbsnp_vcf | File | ||
| reference | String | ||
| readgroups | String[] | ||
| known_indels | File | ||
| downsample_probability | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| downsample |
../tools/downsample.cwl
(CommandLineTool)
|
downsample unaligned BAM | |
| align_workflow |
bam_to_bqsr.cwl
(Workflow)
|
Unaligned BAM to BQSR and VCF |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| mark_duplicates_metrics_file | File |
Permalink:
https://w3id.org/cwl/view/git/5f120e5bc3c0f75bfbc636ea2c6f4393f5d45ca1/definitions/subworkflows/downsampled_alignment.cwl
