Workflow: HS Metrics workflow

Fetched 2023-01-13 15:51:34 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs bam bam collect_summary_hs_metrics collect HS metrics bam->collect_summary_hs_metrics bam collect_per_target_hs_metrics collect HS metrics bam->collect_per_target_hs_metrics bam collect_per_base_hs_metrics collect HS metrics bam->collect_per_base_hs_metrics bam minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->collect_summary_hs_metrics minimum_mapping_quality minimum_mapping_quality->collect_per_target_hs_metrics minimum_mapping_quality minimum_mapping_quality->collect_per_base_hs_metrics minimum_mapping_quality summary_intervals summary_intervals summary_intervals->collect_summary_hs_metrics bait_intervals summary_intervals->collect_summary_hs_metrics output_prefix summary_intervals->collect_summary_hs_metrics target_intervals per_base_intervals per_base_intervals per_base_intervals->collect_per_base_hs_metrics target_intervals per_base_intervals->collect_per_base_hs_metrics bait_intervals per_base_intervals->collect_per_base_hs_metrics output_prefix reference reference reference->collect_summary_hs_metrics reference reference->collect_per_target_hs_metrics reference reference->collect_per_base_hs_metrics reference minimum_base_quality minimum_base_quality minimum_base_quality->collect_summary_hs_metrics minimum_base_quality minimum_base_quality->collect_per_target_hs_metrics minimum_base_quality minimum_base_quality->collect_per_base_hs_metrics minimum_base_quality per_target_intervals per_target_intervals per_target_intervals->collect_per_target_hs_metrics output_prefix per_target_intervals->collect_per_target_hs_metrics target_intervals per_target_intervals->collect_per_target_hs_metrics bait_intervals per_base_coverage_metrics per_base_coverage_metrics per_target_coverage_metrics per_target_coverage_metrics per_target_hs_metrics per_target_hs_metrics per_base_hs_metrics per_base_hs_metrics summary_hs_metrics summary_hs_metrics collect_summary_hs_metrics->summary_hs_metrics collect_per_target_hs_metrics->per_target_coverage_metrics collect_per_target_hs_metrics->per_target_hs_metrics collect_per_base_hs_metrics->per_base_coverage_metrics collect_per_base_hs_metrics->per_base_hs_metrics default1 false default1->collect_summary_hs_metrics per_target_coverage default2 false default2->collect_summary_hs_metrics per_base_coverage default3 false default3->collect_per_target_hs_metrics per_base_coverage default4 true default4->collect_per_target_hs_metrics per_target_coverage default5 false default5->collect_per_base_hs_metrics per_target_coverage default6 true default6->collect_per_base_hs_metrics per_base_coverage
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Inputs

ID Type Title Doc
bam File
reference String
summary_intervals https://w3id.org/cwl/view/git/8438316338e66823e1c9aca9f675b2bf33f2aa59/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/8438316338e66823e1c9aca9f675b2bf33f2aa59/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/8438316338e66823e1c9aca9f675b2bf33f2aa59/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)

Steps

ID Runs Label Doc
collect_summary_hs_metrics
../tools/collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
collect_per_base_hs_metrics
../tools/collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
collect_per_target_hs_metrics
../tools/collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics

Outputs

ID Type Label Doc
summary_hs_metrics File[]
per_base_hs_metrics File[]
per_target_hs_metrics File[]
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
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Permalink: https://w3id.org/cwl/view/git/8438316338e66823e1c9aca9f675b2bf33f2aa59/definitions/subworkflows/hs_metrics.cwl