Workflow: umi molecular alignment workflow
Fetched 2023-01-04 09:53:27 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[] | ||
| omni_vcf | File | ||
| reference | String | ||
| sample_name | String | ||
| bait_intervals | File | ||
| read_structure | String[] | ||
| target_intervals | File | ||
| summary_intervals | https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc |
qc_exome.cwl
(Workflow)
|
Exome QC workflow | |
| alignment |
molecular_alignment.cwl
(Workflow)
|
umi molecular alignment workflow |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| flagstats | File | ||
| hs_metrics | File | ||
| aligned_bam | File | ||
| adapter_histogram | File[] | ||
| duplex_seq_metrics | File[] | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/subworkflows/molecular_qc.cwl
