Workflow: call_cnv.cwl
Fetched 2023-09-14 07:03:31 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 |
|---|---|---|---|
| threads | Integer | ||
| project_name | String | ||
| reference_fasta | File | ||
| tumor_sample_list | File | ||
| normal_sample_list | File | ||
| targets_coverage_bed | File | ||
| targets_coverage_annotation | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| coverage |
../../cwl_tools/cnv/coverage.cwl
(CommandLineTool)
|
||
| copy_number |
../../cwl_tools/cnv/copynumber.cwl
(CommandLineTool)
|
||
| loess_tumor |
../../cwl_tools/cnv/loess.cwl
(CommandLineTool)
|
||
| loess_normal |
../../cwl_tools/cnv/loess.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam_list | File[] | ||
| copy_pdf | File | ||
| seg_files | File[] | ||
| genes_file | File | ||
| probes_file | File | ||
| tumors_covg | File | ||
| normals_covg | File | ||
| intragenic_file | File | ||
| tumor_loess_pdf | File | ||
| normal_loess_pdf | File | ||
| tumor_loess_text | File | ||
| normal_loess_text | File |
Permalink:
https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/workflows/subworkflows/call_cnv.cwl
