Workflow: DAPHNI Consensus Variant Calling
Fetched 2023-01-13 16:20:29 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| Threads | Integer | ||
| TumorBam | File | ||
| NormalBam | File | ||
| Reference | File | ||
| IntervalFile | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| Manta |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Manta.cwl
(CommandLineTool)
|
||
| Lancet |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Lancet.cwl
(CommandLineTool)
|
||
| Mutect2 |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/GATK/GATK-Mutect2.cwl
(CommandLineTool)
|
||
| Strelka |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Strelka2.cwl
(CommandLineTool)
|
||
| Consensus |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Consensus_Caller.cwl
(CommandLineTool)
|
||
| UnzipMutect |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Gunzip.cwl
(CommandLineTool)
|
||
| FilterMutect2 |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/GATK/GATK-FilterMutectCalls.cwl
(CommandLineTool)
|
||
| UnzipStrelkaSNV |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Gunzip.cwl
(CommandLineTool)
|
||
| UnzipStrelkaIndels |
https://gitlab.com/iidsgt/biocwl/raw/master/Tools/Gunzip.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| consensus_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/bca405b31c2413210946e2b7c8773ccc80fc2cf8/Workflows_Release/DAPHNI-Consenus-Variant.cwl
