Workflow: Subworkflow that runs cnvkit in single sample mode and returns a vcf file
Fetched 2023-01-10 17:10:03 GMT
Verified with cwltool version 3.1.20221201130942
- 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 |
|---|---|---|---|
| method | |||
| diagram | Boolean (Optional) | ||
| tumor_bam | File | ||
| scatter_plot | Boolean (Optional) | ||
| reference_cnn | File (Optional) | ||
| male_reference | Boolean (Optional) | ||
| segment_filter | |||
| cnvkit_vcf_name | String | ||
| fasta_reference | File | ||
| drop_low_coverage | Boolean (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cns_to_vcf |
../tools/cnvkit_vcf_export.cwl
(CommandLineTool)
|
Convert default cnvkit .cns output to standard vcf format | |
| cnvkit_main |
../tools/cnvkit_batch.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cn_diagram | File (Optional) | ||
| cnvkit_vcf | File | ||
| cn_scatter_plot | File (Optional) | ||
| tumor_target_coverage | File | ||
| tumor_bin_level_ratios | File | ||
| tumor_segmented_ratios | File | ||
| tumor_antitarget_coverage | File |
Permalink:
https://w3id.org/cwl/view/git/10870aefd20469e728969269ff3c54b3b8339a18/definitions/subworkflows/cnvkit_single_sample.cwl
