Workflow: abra_workflow.cwl
Fetched 2024-05-04 16:31:08 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
| patient_id | String | ||
| abra__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/abra.yaml#abra__params | ||
| fci__basq_fix | Boolean (Optional) | ||
| reference_fasta | String | ||
| fix_mate_information__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/fix_mate_information.yaml#fix_mate_information__params | ||
| find_covered_intervals__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/find_covered_intervals.yaml#find_covered_intervals__params |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| abra |
../../cwl_tools/abra/abra.cwl
(CommandLineTool)
|
||
| list2bed |
../../cwl_tools/python/list2bed.cwl
(CommandLineTool)
|
||
| parallel_fixmate | |||
| find_covered_intervals |
../../cwl_tools/gatk/FindCoveredIntervals.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| ir_bams | File[] | ||
| covint_bed | File | ||
| covint_list | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/ABRA/abra_workflow.cwl
