- 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