Workflow: snp_callers_workflow.cwl
Fetched 2023-01-09 06:22:36 GMT
Verified with cwltool version 3.1.20221201130942
A workflow for running MuSe, MuTect, SomaticSniper, and Pindel. See [the github repository](https://github.com/BD2KGenomics/dockstore_workflow_snps) for details.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| CPUS | Integer | ||
| MODE | String | ||
| GENO_FA | File | ||
| DBSNP_VCF | File | ||
| TUMOR_BAM | File | ||
| COSMIC_VCF | File | ||
| NORMAL_BAM | File | ||
| CENTROMERE_BED | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| tar |
tar.cwl
(CommandLineTool)
|
||
| muse |
muse.cwl
(CommandLineTool)
|
MuSE | |
| mutect |
mutect.cwl
(CommandLineTool)
|
MuTect | |
| pindel |
pindel.cwl
(CommandLineTool)
|
Pindel-Somatic | |
| muse_filter |
muse_filter.cwl
(CommandLineTool)
|
Filter MuSE | |
| somaticsniper |
somatic_sniper.cwl
(CommandLineTool)
|
SomaticSniper |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| OUTPUT | File |
Permalink:
https://w3id.org/cwl/view/git/8c8217b63d16c13924a00408e2b621d888b0aaa5/snp_callers_workflow.cwl
