Workflow: call_variants.cwl
Fetched 2024-06-11 00:17:00 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 |
|---|---|---|---|
| dbsnp | File | ||
| cosmic | File | ||
| bed_file | File | ||
| run_tools | https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/resources/schemas/variants_tools.yaml#run_tools | ||
| tumor_bam | File | ||
| normal_bam | File | ||
| mutect_params | https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/resources/schemas/params/mutect.yaml#mutect_params | ||
| vardict_params | https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/resources/schemas/params/vardict.yaml#vardict_params | ||
| reference_fasta | File | ||
| tumor_sample_name | String | ||
| normal_sample_name | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| mutect |
../../cwl_tools/mutect/mutect.cwl
(CommandLineTool)
|
||
| vardict |
../../cwl_tools/vardict/vardict_paired.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| mutect_vcf | File | ||
| vardict_vcf | File | ||
| mutect_callstats | File |
Permalink:
https://w3id.org/cwl/view/git/3441040dfaecba58150c13a95a6a93657b00778a/workflows/subworkflows/call_variants.cwl
