Workflow: downsample unaligned BAM and align
Fetched 2023-01-03 23:23:15 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- Default Values
- Nested Workflows
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- 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[] | ||
| reference | String | ||
| readgroups | String[] | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| 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 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| mark_duplicates_metrics_file | File |
Permalink:
https://w3id.org/cwl/view/git/ece70ac30cd87100a70f7dc64d08fa72724e9416/definitions/subworkflows/downsampled_alignment.cwl
