Workflow: WGS QC workflow

Fetched 2024-02-28 23:47:32 GMT
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Inputs

ID Type Title Doc
bam File
omni_vcf File
intervals File
reference File
sample_name String (Optional)
summary_intervals https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
verify_bam_id
../tools/verify_bam_id.cwl (CommandLineTool)
verify BAM ID
samtools_flagstat
../tools/samtools_flagstat.cwl (CommandLineTool)
samtools flagstat
collect_hs_metrics
hs_metrics.cwl (Workflow)
HS Metrics workflow
collect_wgs_metrics
../tools/collect_wgs_metrics.cwl (CommandLineTool)
collect WGS metrics
collect_gc_bias_metrics
../tools/collect_gc_bias_metrics.cwl (CommandLineTool)
collect gc bias metrics
collect_insert_size_metrics
../tools/collect_insert_size_metrics.cwl (CommandLineTool)
collect insert size metrics
collect_alignment_summary_metrics
../tools/collect_alignment_summary_metrics.cwl (CommandLineTool)
collect alignment summary metrics

Outputs

ID Type Label Doc
flagstats File
wgs_metrics File
gc_bias_metrics File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
gc_bias_metrics_chart File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
gc_bias_metrics_summary File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/233f026ffce240071edda526391be0c03186fce8/definitions/subworkflows/qc_wgs.cwl