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subworkflows_qc_exome.cwl
Travis CI User edited this page Dec 4, 2019
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Exome QC workflow
| 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[] |
| 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 |
| Name | CWL Run |
|---|---|
| collect_insert_size_metrics | tools/collect_insert_size_metrics.cwl |
| collect_alignment_summary_metrics | tools/collect_alignment_summary_metrics.cwl |
| collect_roi_hs_metrics | tools/collect_hs_metrics.cwl |
| collect_detailed_hs_metrics | subworkflows/hs_metrics.cwl |
| samtools_flagstat | tools/samtools_flagstat.cwl |
| select_variants | tools/select_variants.cwl |
| verify_bam_id | tools/verify_bam_id.cwl |