Workflow: WGS QC workflow
Fetched 2023-01-04 07:48:26 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
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- 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 | ||
| intervals | File | ||
| reference | String | ||
| summary_intervals | https://w3id.org/cwl/view/git/dc2c019c1aa24cc01b451a0f048cf94a35f163c4/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/dc2c019c1aa24cc01b451a0f048cf94a35f163c4/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/dc2c019c1aa24cc01b451a0f048cf94a35f163c4/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| verify_bam_id |
../tools/verify_bam_id.cwl
(CommandLineTool)
|
verify BAM ID | |
| samtools_flagstat |
../tools/samtools_flagstat.cwl
(CommandLineTool)
|
samtools flagstat | |
| collect_hs_metrics |
hs_metrics.cwl
(Workflow)
|
HS Metrics workflow | |
| collect_wgs_metrics |
../tools/collect_wgs_metrics.cwl
(CommandLineTool)
|
collect WGS metrics | |
| deeptools_bamcoverage |
../tools/deeptools_bamcoverage.cwl
(CommandLineTool)
|
deepTools bamCoverage | |
| collect_gc_bias_metrics |
../tools/collect_gc_bias_metrics.cwl
(CommandLineTool)
|
collect gc bias metrics | |
| 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 | ||
| wgs_metrics | File | ||
| gc_bias_metrics | File | ||
| bamcoverage_bigwig | File | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| gc_bias_metrics_chart | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_metrics | File | ||
| gc_bias_metrics_summary | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/dc2c019c1aa24cc01b451a0f048cf94a35f163c4/definitions/subworkflows/qc_wgs.cwl
