- 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 |
---|---|---|---|
bam | File | ||
ploidy | Integer (Optional) | ||
dbsnp_vcf | File (Optional) | ||
intervals | ca57bd8159c2e79467ba0e864fa8cb46[] | ||
reference | File | ||
read_filter | String (Optional) | ||
gvcf_gq_bands | String[] | ||
output_prefix | String (Optional) |
an optional string to prepend to the output filename |
|
max_alternate_alleles | Integer (Optional) | ||
contamination_fraction | String (Optional) | ||
emit_reference_confidence |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
haplotype_caller |
../tools/gatk_haplotype_caller.cwl
(CommandLineTool)
|
GATK HaplotypeCaller |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
gvcf | File[] |
Permalink:
https://w3id.org/cwl/view/git/889a077a20c0fdb01f4ed97aa4bc40f920c37a1a/definitions/subworkflows/gatk_haplotypecaller_iterator.cwl