Workflow: exome alignment with qc
Fetched 2025-11-11 14:48:28 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bams | File[] | ||
| dbsnp | File | ||
| mills | File | ||
| omni_vcf | File | ||
| reference | String | ||
| readgroups | String[] | ||
| known_indels | File | ||
| bait_intervals | File | ||
| target_intervals | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc | Exome QC workflow | ||
| alignment |
exome_alignment_packed.cwl#workflow.cwl_2
(Workflow)
|
Unaligned BAM to BQSR and VCF |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| flagstats | File | ||
| hs_metrics | File | ||
| insert_size_metrics | File | ||
| verify_bam_id_depth | File | ||
| verify_bam_id_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_target_coverage_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/0ae2468ab2ba0b9a196c2aa89b580555750bf0f6/workflows/hello/exome_alignment_packed.cwl?part=main
