Workflow: Exome QC workflow
Fetched 2023-01-11 13:57:15 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 | File | ||
| bait_intervals | File | ||
| target_intervals | File | ||
| summary_intervals | https://w3id.org/cwl/view/git/b9e7392e72506cadd898a6ac4db330baf6535ab6/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/b9e7392e72506cadd898a6ac4db330baf6535ab6/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/b9e7392e72506cadd898a6ac4db330baf6535ab6/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| verify_bam_id |
../tools/verify_bam_id.cwl
(CommandLineTool)
|
verify BAM ID | |
| select_variants |
../tools/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
| samtools_flagstat |
../tools/samtools_flagstat.cwl
(CommandLineTool)
|
samtools flagstat | |
| collect_roi_hs_metrics |
../tools/collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics | |
| collect_detailed_hs_metrics |
hs_metrics.cwl
(Workflow)
|
HS Metrics workflow | |
| collect_insert_size_metrics |
../tools/collect_insert_size_metrics.cwl
(CommandLineTool)
|
collect insert size metrics | |
| collect_alignment_summary_metrics |
../tools/collect_alignment_summary_metrics.cwl
(CommandLineTool)
|
collect alignment summary metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| flagstats | File | ||
| hs_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/b9e7392e72506cadd898a6ac4db330baf6535ab6/definitions/subworkflows/qc_exome.cwl
