Workflow: dedup-3-pass-distr.cwl
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)
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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