Workflow: dedup-3-pass-distr.cwl
Fetched 2023-04-17 14:16:48 GMT
Verified with cwltool version 3.1.20230201224320
run 3-pass dedup: algo LocusCollector + algo Dedup output_dup_read_name + algo Dedup dedup_by_read_name sequentially in distributed mode
- Selected
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- 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) | ||
| interval | File (Optional) | ||
| input_bam | File[] | ||
| reference | File (Optional) | ||
| output_file | String | ||
| advanced_options | |||
| metrics_output_file | String |
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 |
|
| dedup_pre |
../algo/dedup_pre.cwl
(CommandLineTool)
|
||
| dup_read_name |
../algo/dedup.cwl
(CommandLineTool)
|
||
| merge_metrics |
../algo/dedup.cwl
(CommandLineTool)
|
||
| dedup_by_read_name |
../algo/dedup.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output | File | ||
| metrics_output | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/stage/dedup-3-pass-distr.cwl
