Workflow: filtering.cwl
Fetched 2024-05-19 12:46:49 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 |
|---|---|---|---|
| ref_fasta | File | ||
| mutect_vcf | File | ||
| vardict_vcf | File | ||
| mutect_callstats | File | ||
| tumor_sample_name | String | ||
| normal_sample_name | String | ||
| basicfiltering_mutect_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/basic-filtering-mutect.yaml#basicfiltering_mutect_params | ||
| basicfiltering_vardict_params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/basic-filtering-vardict.yaml#basicfiltering_vardict_params |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mutect_filtering_step |
../../cwl_tools/basicfiltering/basic-filtering_mutect.cwl
(CommandLineTool)
|
Filter snps from the output of muTect |
|
| vardict_filtering_step |
../../cwl_tools/basicfiltering/basic-filtering_vardict.cwl
(CommandLineTool)
|
Filter snps/indels from the output of vardict |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mutect_norm_vcf | File | ||
| vardict_norm_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/subworkflows/filtering.cwl
