- 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 | ||
vcf | File | ||
sample | String | ||
reference_fasta | File | ||
min_base_quality | Integer (Optional) | ||
min_mapping_quality | Integer (Optional) |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
decompose_variants |
../tools/vt_decompose.cwl
(CommandLineTool)
|
run vt decompose | |
normalize_variants |
../tools/normalize_variants.cwl
(CommandLineTool)
|
Normalize variants |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
normalized_vcf | File | ||
snv_bam_readcount_tsv | File | ||
indel_bam_readcount_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/3034168d652bfa930ba09af20e473a4564a8010d/definitions/subworkflows/bam_readcount.cwl