Workflow: preparation_workflow.cwl
Fetched 2024-05-09 20:08:16 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 |
|---|---|---|---|
| has_normal | Integer[] | ||
| pon_calling | Integer[] | ||
| tumor_gdc_id | String | ||
| normal_gdc_id | String (Optional) | ||
| bioclient_config | File | ||
| tumor_index_gdc_id | String | ||
| normal_index_gdc_id | String (Optional) | ||
| reference_fa_gdc_id | String | ||
| reference_fai_gdc_id | String | ||
| reference_dict_gdc_id | String | ||
| panel_of_normal_gdc_id | String (Optional) | ||
| reference_image_gdc_id | String (Optional) | ||
| germline_resource_gdc_id | String (Optional) | ||
| panel_of_normal_index_gdc_id | String (Optional) | ||
| germline_resource_index_gdc_id | String (Optional) | ||
| common_biallelic_variants_gdc_id | String (Optional) | ||
| common_biallelic_variants_index_gdc_id | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| stage |
stage_workflow.cwl
(Workflow)
|
||
| extract_normal |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| tumor_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| normal_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_normal_index |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| tumor_index_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| normal_index_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| reference_fa_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| reference_fai_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_panel_of_normal |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| extract_reference_image |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| reference_dict_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_common_biallelic |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| panel_of_normal_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| reference_image_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_germline_resource |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| germline_resource_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_panel_of_normal_index |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| extract_common_biallelic_index |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| panel_of_normal_index_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| extract_germline_resource_index |
../extract_from_conditional_array.cwl
(ExpressionTool)
|
||
| germline_resource_index_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| common_biallelic_variants_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
||
| common_biallelic_variants_index_download |
../bio_client/bio_client_download.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| reference_image | File (Optional) | ||
| tumor_with_index | File | ||
| normal_with_index | File (Optional) | ||
| reference_with_index | File | ||
| panel_of_normal_with_index | File (Optional) | ||
| germline_resource_with_index | File (Optional) | ||
| common_biallelic_variants_with_index | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/58b62b1bf329b3fbffbd5d9080709999bebc1763/utils-cwl/subworkflow/preparation_workflow.cwl
