- 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 |
---|---|---|---|
vcf | File | ||
cram | File | ||
reference | String | ||
variant_caller | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
fp_bgzip |
../detect_variants/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
fp_index |
../detect_variants/index.cwl
(CommandLineTool)
|
vcf index | |
fp_filter |
fp_filter.cwl
(CommandLineTool)
|
False Positive filter | |
cram_to_bam |
../cram_to_bam/workflow.cwl
(Workflow)
|
cram_to_bam workflow | |
hard_filter |
../detect_variants/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
normalize_variants |
normalize_variants.cwl
(CommandLineTool)
|
Normalize variants |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
filtered_vcf | File | ||
unfiltered_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/be7e682c6a2d0b24b949e022aeae7786bd8434ed/fp_filter/workflow.cwl