Workflow: Add snv and indel bam-readcount files to a vcf
Fetched 2026-03-09 00:19:49 GMT
Verified with cwltool version 3.1.20230201224320
- 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 | ||
| data_type | |||
| sample_name | String | ||
| snv_bam_readcount_tsv | File | ||
| indel_bam_readcount_tsv | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| add_snv_bam_readcount_to_vcf |
../tools/vcf_readcount_annotator.cwl
(CommandLineTool)
|
add bam_readcount info to vcf | |
| add_indel_bam_readcount_to_vcf |
../tools/vcf_readcount_annotator.cwl
(CommandLineTool)
|
add bam_readcount info to vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| annotated_bam_readcount_vcf | File |
Permalink:
https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/subworkflows/vcf_readcount_annotator.cwl
