Workflow: facets-suite-workflow.cwl
Fetched 2023-01-03 21:39:30 GMT
Verified with cwltool version 3.1.20221201130942
Workflow for running the facets suite workflow on a single tumor normal pair Includes handling of errors in case execution fails for the sample pair
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| pair_id | String | ||
| pair_maf | File | ||
| tumor_id | String | ||
| normal_id | String | ||
| snp_pileup | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| run_facets |
run-facets-wrapper.cwl
(CommandLineTool)
|
||
| update_maf |
update_cBioPortal_data.cwl
(CommandLineTool)
|
||
| annotate_maf |
annotate-maf-wrapper.cwl
(CommandLineTool)
|
||
| check_results |
facets-suite-workflow.cwl#check_results/check_results
(ExpressionTool)
|
||
| check_run_facets |
facets-suite-workflow.cwl#check_run_facets/check_facets
(ExpressionTool)
|
||
| check_update_maf |
facets-suite-workflow.cwl#check_update_maf/check_update_maf
(ExpressionTool)
|
||
| label_maf_normal |
paste-col-wrapper.cwl
(CommandLineTool)
|
||
| label_maf_sample |
paste-col-wrapper.cwl
(CommandLineTool)
|
||
| run_facets_legacy |
run-facets-legacy-wrapper.cwl
(CommandLineTool)
|
||
| check_annotate_maf |
facets-suite-workflow.cwl#check_annotate_maf/check_annotate_maf
(ExpressionTool)
|
||
| check_label_maf_normal |
facets-suite-workflow.cwl#check_label_maf_normal/check_label_maf_normal
(ExpressionTool)
|
||
| check_label_maf_sample |
facets-suite-workflow.cwl#check_label_maf_sample/check_label_maf_sample
(ExpressionTool)
|
||
| label_facets_txt_tumor |
paste-col-wrapper.cwl
(CommandLineTool)
|
||
| check_run_facets_legacy |
facets-suite-workflow.cwl#check_run_facets_legacy/check_facets_legacy
(ExpressionTool)
|
||
| label_facets_txt_normal |
paste-col-wrapper.cwl
(CommandLineTool)
|
||
| check_label_facets_txt_tumor |
facets-suite-workflow.cwl#check_label_facets_txt_tumor/check_label_facets_txt_tumor
(ExpressionTool)
|
||
| check_label_facets_txt_normal |
facets-suite-workflow.cwl#check_label_facets_txt_normal/check_label_facets_txt_normal
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| qc_txt | File (Optional) | ||
| pair_id | String | ||
| facets_txt | File (Optional) | ||
| hisens_rds | File (Optional) | ||
| hisens_seg | File (Optional) | ||
| output_dir | Directory | ||
| purity_rds | File (Optional) | ||
| purity_seg | File (Optional) | ||
| annotated_maf | File (Optional) | ||
| arm_level_txt | File (Optional) | ||
| gene_level_txt | File (Optional) | ||
| results_passed | Boolean | ||
| hisens_cncf_txt | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/7eb2b0a4d37018142233d770595ac2e00376dab4/cwl/facets-suite-workflow.cwl
