Workflow: Exome QC workflow
Fetched 2025-11-01 15:48:30 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 |
|---|---|---|---|
| cram | File | ||
| omni_vcf | File | ||
| reference | String | ||
| bait_intervals | File | ||
| target_intervals | File | ||
| per_base_intervals | File | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | File | ||
| minimum_mapping_quality | Integer (Optional) | ||
| per_base_bait_intervals | File | ||
| per_target_bait_intervals | File | ||
| picard_metric_accumulation_level | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cram_to_bam |
../cram_to_bam/workflow.cwl
(Workflow)
|
cram_to_bam workflow | |
| verify_bam_id |
verify_bam_id.cwl
(CommandLineTool)
|
verify BAM ID | |
| select_variants |
../detect_variants/select_variants.cwl
(CommandLineTool)
|
SelectVariants (GATK 3.6) | |
| samtools_flagstat |
samtools_flagstat.cwl
(CommandLineTool)
|
samtools flagstat | |
| collect_roi_hs_metrics |
collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics | |
| collect_insert_size_metrics |
collect_insert_size_metrics.cwl
(CommandLineTool)
|
collect insert size metrics | |
| collect_per_base_hs_metrics |
collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics | |
| collect_per_target_hs_metrics |
collect_hs_metrics.cwl
(CommandLineTool)
|
collect HS metrics | |
| collect_alignment_summary_metrics |
collect_alignment_summary_metrics.cwl
(CommandLineTool)
|
collect alignment summary metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| flagstats | File | ||
| hs_metrics | File | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File (Optional) | ||
| verify_bam_id_depth | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File (Optional) | ||
| verify_bam_id_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File (Optional) | ||
| per_target_coverage_metrics | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/qc/workflow_exome.cwl
