Workflow: stage_workflow.cwl
Fetched 2024-05-20 18:02:03 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| pon | File (Optional) | ||
| tumor | File | ||
| normal | File (Optional) | ||
| pon_index | File (Optional) | ||
| reference | File | ||
| has_normal | Integer[] | ||
| pon_calling | Integer[] | ||
| tumor_index | File | ||
| germline_ref | File (Optional) | ||
| normal_index | File (Optional) | ||
| biallelic_ref | File (Optional) | ||
| reference_fai | File | ||
| reference_dict | File | ||
| germline_ref_index | File (Optional) | ||
| biallelic_ref_index | File (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| make_pon |
../make_secondary.cwl
(CommandLineTool)
|
||
| extract_pon |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| extract_normal |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| make_reference |
../make_secondary.cwl
(CommandLineTool)
|
||
| make_tumor_bam |
../make_secondary.cwl
(CommandLineTool)
|
||
| make_normal_bam |
../make_secondary.cwl
(CommandLineTool)
|
||
| make_germline_ref |
../make_secondary.cwl
(CommandLineTool)
|
||
| make_biallelic_ref |
../make_secondary.cwl
(CommandLineTool)
|
||
| extract_germline_ref |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| extract_biallelic_ref |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| standardize_tumor_bai |
../rename_file.cwl
(CommandLineTool)
|
Renames the file |
|
| standardize_normal_bai |
../rename_file.cwl
(CommandLineTool)
|
Renames the file |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| pon_with_index | File (Optional) | ||
| tumor_with_index | File | ||
| normal_with_index | File (Optional) | ||
| reference_with_index | File | ||
| germline_ref_with_index | File (Optional) | ||
| biallelic_ref_with_index | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/58b62b1bf329b3fbffbd5d9080709999bebc1763/utils-cwl/subworkflow/stage_workflow.cwl
