Workflow: WGS QC workflow

Fetched 2019-05-20 22:40:15 GMT
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Inputs

ID Type Title Doc
reference File
omni_vcf File
intervals File
bam File

Steps

ID Runs Label Doc
collect_alignment_summary_metrics
collect_alignment_summary_metrics.cwl (CommandLineTool)
collect alignment summary metrics
collect_insert_size_metrics
collect_insert_size_metrics.cwl (CommandLineTool)
collect insert size metrics
collect_gc_bias_metrics
collect_gc_bias_metrics.cwl (CommandLineTool)
collect gc bias metrics
samtools_flagstat
samtools_flagstat.cwl (CommandLineTool)
samtools flagstat
collect_wgs_metrics
collect_wgs_metrics.cwl (CommandLineTool)
collect WGS metrics
verify_bam_id
verify_bam_id.cwl (CommandLineTool)
verify BAM ID

Outputs

ID Type Label Doc
gc_bias_metrics File
gc_bias_metrics_chart File
wgs_metrics File
insert_size_metrics File
verify_bam_id_metrics File
alignment_summary_metrics File
gc_bias_metrics_summary File
verify_bam_id_depth File
flagstats File
Permalink: https://w3id.org/cwl/view/git/5a67e91727c8eb44afff27f9e4774eafef579c58/qc/workflow_wgs.cwl