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subworkflows_qc_exome_no_verify_bam.cwl
Travis CI User edited this page Feb 24, 2021
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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 | |||
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 |
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 |