- 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/4cded2c595b2ff83046729cd230f5ad34be3137d/detect_variants/detect_variants.cwl