Workflow: Detect Variants workflow
Fetched 2023-01-04 23:30:50 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 |
|---|---|---|---|
| dbsnp_vcf | File (Optional) | ||
| reference | File | ||
| tumor_bam | File | ||
| cosmic_vcf | File (Optional) | ||
| normal_bam | File | ||
| interval_list | File | ||
| pindel_insert_size | Integer | ||
| strelka_exome_mode | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bgzip |
bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index |
index.cwl
(CommandLineTool)
|
vcf index | |
| filter |
fp_filter.cwl
(CommandLineTool)
|
False Positive filter | |
| mutect |
../mutect/workflow.cwl
(Workflow)
|
mutect parallel workflow | |
| pindel |
../pindel/workflow.cwl
(Workflow)
|
pindel parallel workflow | |
| combine |
combine_variants.cwl
(CommandLineTool)
|
CombineVariants (GATK 3.6) | |
| strelka |
../strelka/workflow.cwl
(Workflow)
|
strelka workflow | |
| varscan |
../varscan/workflow.cwl
(Workflow)
|
Varscan Workflow |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/5a67e91727c8eb44afff27f9e4774eafef579c58/detect_variants/detect_variants.cwl
