subworkflows_qc_exome.cwl - genome/analysis-workflows GitHub Wiki
Documentation for qc_exome.cwl
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Overview
Exome QC workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| bam |
|
|
File |
['^.bai'] |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| bait_intervals |
|
|
File |
|
| target_intervals |
|
|
File |
|
| omni_vcf |
|
|
File |
['.tbi'] |
| picard_metric_accumulation_level |
|
|
string |
|
| minimum_mapping_quality |
|
|
int? |
|
| minimum_base_quality |
|
|
int? |
|
| per_base_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| per_target_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| summary_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| insert_size_metrics |
|
|
File |
|
| insert_size_histogram |
|
|
File |
|
| alignment_summary_metrics |
|
|
File |
|
| hs_metrics |
|
|
File |
|
| per_target_coverage_metrics |
|
|
File[] |
|
| per_target_hs_metrics |
|
|
File[] |
|
| per_base_coverage_metrics |
|
|
File[] |
|
| per_base_hs_metrics |
|
|
File[] |
|
| summary_hs_metrics |
|
|
File[] |
|
| flagstats |
|
|
File |
|
| verify_bam_id_metrics |
|
|
File |
|
| verify_bam_id_depth |
|
|
File |
|
Steps