Workflow: bwameth_align_merge_sort_dedup.cwl
Fetched 2025-12-14 14:17:22 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref | File | ||
| pbat | Boolean | ||
| read1 | File[] |
first reads belonging to the same library |
|
| read2 | File[] |
first reads belonging to the same library |
|
| threads | Integer | ||
| output_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwameth_align |
bwameth_align.cwl
(CommandLineTool)
|
||
| merge_and_sort |
/cwl/view/git/1416ade270d1b990087e39c6680464c12cf564cc/tools/samtools_merge_and_sort.cwl
(CommandLineTool)
|
||
| picard_markdup |
/cwl/view/git/1416ade270d1b990087e39c6680464c12cf564cc/tools/picard_markdup.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_duprem | File | ||
| picard_markdup_log | File | ||
| picard_markdup_stat | File |
Permalink:
https://w3id.org/cwl/view/git/1416ade270d1b990087e39c6680464c12cf564cc/workflows/bwameth/tools/bwameth_align_merge_sort_dedup.cwl
