Workflow: Exome QC workflow

Fetched 2021-09-21 23:29:45 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
per_target_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
reference String
omni_vcf File
bait_intervals File
picard_metric_accumulation_level String (Optional)
per_base_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)
target_intervals File
summary_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
bam File
minimum_base_quality Integer (Optional)

Steps

ID Runs Label Doc
collect_alignment_summary_metrics
../tools/collect_alignment_summary_metrics.cwl (CommandLineTool)
collect alignment summary metrics
select_variants
../tools/select_variants.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
collect_insert_size_metrics
../tools/collect_insert_size_metrics.cwl (CommandLineTool)
collect insert size metrics
collect_roi_hs_metrics
../tools/collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
samtools_flagstat
../tools/samtools_flagstat.cwl (CommandLineTool)
samtools flagstat
collect_detailed_hs_metrics
hs_metrics.cwl (Workflow)
HS Metrics workflow
verify_bam_id
../tools/verify_bam_id.cwl (CommandLineTool)
verify BAM ID

Outputs

ID Type Label Doc
per_target_coverage_metrics File[]
hs_metrics File
verify_bam_id_metrics File
alignment_summary_metrics File
per_base_hs_metrics File[]
insert_size_metrics File
per_target_hs_metrics File[]
insert_size_histogram File
verify_bam_id_depth File
flagstats File
summary_hs_metrics File[]
per_base_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/qc_exome.cwl