- 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 |
---|---|---|---|
reference | File | ||
tumor_bam | File | ||
normal_bam | File (Optional) | ||
interval_list | File | ||
scatter_count | Integer | ||
tumor_sample_name | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
merge |
../tools/merge_vcf.cwl
(CommandLineTool)
|
vcf merge | |
filter |
fp_filter.cwl
(Workflow)
|
fp_filter workflow | |
mutect |
../tools/mutect.cwl
(CommandLineTool)
|
Mutect2 (GATK 4) | |
split_interval_list |
../tools/split_interval_list.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
filtered_vcf | File | ||
unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a/definitions/subworkflows/mutect.cwl