Workflow: bam_readcount workflow
Fetched 2025-09-08 06:01:03 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 |
|---|---|---|---|
| bam | File | ||
| vcf | File | ||
| sample | String | ||
| reference_fasta | String | ||
| 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/86fbeb95ef85111f3b4c6bc2bba8f06cef64e157/definitions/subworkflows/bam_readcount.cwl
