- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
snp_mode | String | ||
reference | File |
reference human genome file |
|
indel_mode | String | ||
snpf_genome | String | ||
haplotest_vcf | File | ||
resource_omni | File | ||
snpf_data_dir | Directory | ||
resource_dbsnp | File | ||
resource_mills | File | ||
resource_hapmap | File | ||
snpf_nodownload | Boolean |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
vqsr_indels |
../../tools/GATK-VariantRecalibrator-Indels.cwl
(CommandLineTool)
|
GATK-VariantsRecalibrator.cwl is developed for CWL consortium |
|
snpeff_indels |
../../tools/snpEff.cwl
(CommandLineTool)
|
||
apply_recalibration_indels |
../../tools/GATK-ApplyRecalibration.cwl
(CommandLineTool)
|
Outputs
ID | Type | Label | Doc |
---|---|---|---|
recal_File | File | ||
annotated_indels | File |
https://w3id.org/cwl/view/git/8e841da119480fdc626dedca572e55d15f9b017f/workflows/GATK/GATK-Sub-Workflow-h3abionet-indel.cwl