subworkflows_qc_wgs_nonhuman.cwl
Travis CI User edited this page Feb 24, 2021
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WGS QC workflow nonhuman
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| bam | File | ['^.bai', '.bai'] | ||
| reference | ['string', 'File'] | ['.fai', '^.dict'] | ||
| 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 | |||
| gc_bias_metrics | File | |||
| wgs_metrics | File | |||
| gc_bias_metrics_chart | File | |||
| gc_bias_metrics_summary | File | |||
| flagstats | File | |||
| per_base_coverage_metrics | File[] | |||
| per_base_hs_metrics | File[] | |||
| per_target_coverage_metrics | File[] | |||
| per_target_hs_metrics | File[] | |||
| summary_hs_metrics | File[] | |||
| bamcoverage_bigwig | 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_gc_bias_metrics | tools/collect_gc_bias_metrics.cwl |
| collect_wgs_metrics | tools/collect_wgs_metrics.cwl |
| samtools_flagstat | tools/samtools_flagstat.cwl |
| collect_hs_metrics | subworkflows/hs_metrics.cwl |
| cgpbigwig_bamcoverage | tools/bam_to_bigwig.cwl |