Workflow: Detect whitelisted variants
Fetched 2024-11-25 23:52:29 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reference | File | ||
| tumor_bam | File | ||
| normal_bam | File | ||
| min_coverage | Integer | ||
| min_var_freq | Float | ||
| interval_list | File | ||
| whitelist_vcf | File | ||
| filter_whitelist_variants | Boolean |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| bgzip2 |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| index2 |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| decompose |
../tools/vt_decompose.cwl
(CommandLineTool)
|
run vt decompose | |
| whitelist_filter |
../tools/filter_vcf_whitelist.cwl
(CommandLineTool)
|
Filter variants from the whitelist detector | |
| GATK_haplotype_caller |
../tools/whitelist_gatk_haplotype_caller.cwl
(CommandLineTool)
|
HaplotypeCaller (GATK4) |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| whitelist_variants_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/656d9ae18f164f983c5672bcf51037cd73309f4f/subworkflows/whitelist.cwl
