Workflow: Bisulfite QC tools
Fetched 2023-01-03 20:32:51 GMT
Verified with cwltool version 3.1.20221201130942
- 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 | ||
| reference | String | ||
| output_dir | String | ||
| QCannotation | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| coverage_stats |
../tools/bisulfite_qc_coverage_stats.cwl
(CommandLineTool)
|
Biscuit QC: Bisulfite conversion rate. | |
| mapping_summary |
../tools/bisulfite_qc_mapping_summary.cwl
(CommandLineTool)
|
Biscuit QC: Bisulfite conversion rate. | |
| bisulfite_conversion |
../tools/bisulfite_qc_conversion.cwl
(CommandLineTool)
|
Biscuit QC: Bisulfite conversion rate. | |
| gather_to_sub_directory |
../tools/gather_to_sub_directory.cwl
(CommandLineTool)
|
||
| cpg_retention_distribution |
../tools/bisulfite_qc_cpg_retention_distribution.cwl
(CommandLineTool)
|
Biscuit QC: CpG Retention Distribution |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| QC_directory | Directory |
Permalink:
https://w3id.org/cwl/view/git/061d3a2fbcd8a1c39c0b38c549e528deb24a9d54/definitions/subworkflows/bisulfite_qc.cwl
