Workflow: realign-distr.cwl
Fetched 2023-01-12 19:55:38 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:
BSD 2-clause "Simplified" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| shard | String[] | ||
| threads | Integer (Optional) | ||
| input_bam | File[] | ||
| reference | File | ||
| known_sites | File[] (Optional) | ||
| output_file | String | ||
| interval_list | File (Optional) | ||
| advanced_options | String[] (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| merge |
../algo/bam-merge.cwl
(CommandLineTool)
|
merge sorted bam files. If input bam files are in the order of coordinate, and no overlap, mergemode 10 can be used |
|
| realign |
../algo/realign.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/stage/realign-distr.cwl
