Workflow: WGS QC workflow
Fetched 2026-01-27 06:52:41 GMT
Verified with cwltool version 3.1.20230201224320
- 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 | ||
| intervals | File | ||
| reference | String | ||
| 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 | |
| samtools_flagstat |
samtools_flagstat.cwl
(CommandLineTool)
|
samtools flagstat | |
| collect_wgs_metrics |
collect_wgs_metrics.cwl
(CommandLineTool)
|
collect WGS metrics | |
| collect_gc_bias_metrics |
collect_gc_bias_metrics.cwl
(CommandLineTool)
|
collect gc bias metrics | |
| collect_insert_size_metrics |
collect_insert_size_metrics.cwl
(CommandLineTool)
|
collect insert size metrics | |
| collect_alignment_summary_metrics |
collect_alignment_summary_metrics.cwl
(CommandLineTool)
|
collect alignment summary metrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| flagstats | File | ||
| wgs_metrics | File | ||
| gc_bias_metrics | File | ||
| insert_size_metrics | File | ||
| verify_bam_id_depth | File | ||
| gc_bias_metrics_chart | File | ||
| insert_size_histogram | File | ||
| verify_bam_id_metrics | File | ||
| gc_bias_metrics_summary | File | ||
| alignment_summary_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/e497d1553498eb1c6daecf242ed4fa1375a892fd/qc/workflow_wgs.cwl
