Workflow: Exome QC workflow

Fetched 2021-06-17 21:27:27 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
per_target_intervals File
reference String
omni_vcf File
picard_metric_accumulation_level String (Optional)
bait_intervals File
per_base_bait_intervals File
cram File
per_base_intervals File
minimum_mapping_quality Integer (Optional)
target_intervals File
minimum_base_quality Integer (Optional)
per_target_bait_intervals File

Steps

ID Runs Label Doc
collect_alignment_summary_metrics
collect_alignment_summary_metrics.cwl (CommandLineTool)
collect alignment summary metrics
cram_to_bam cram_to_bam workflow
collect_insert_size_metrics
collect_insert_size_metrics.cwl (CommandLineTool)
collect insert size metrics
collect_per_base_hs_metrics
collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
select_variants
../detect_variants/select_variants.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
collect_roi_hs_metrics
collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
samtools_flagstat
samtools_flagstat.cwl (CommandLineTool)
samtools flagstat
verify_bam_id
verify_bam_id.cwl (CommandLineTool)
verify BAM ID
collect_per_target_hs_metrics
collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics

Outputs

ID Type Label Doc
per_target_coverage_metrics File (Optional)
hs_metrics File
per_base_hs_metrics File (Optional)
verify_bam_id_metrics File
alignment_summary_metrics File
insert_size_metrics File
per_target_hs_metrics File (Optional)
insert_size_histogram File
verify_bam_id_depth File
flagstats File
per_base_coverage_metrics File (Optional)
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/qc/workflow_exome.cwl