Workflow: Exome QC workflow

Fetched 2023-01-14 17:36:53 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs target_intervals target_intervals select_variants SelectVariants (GATK 3.6) target_intervals->select_variants interval_list collect_roi_hs_metrics collect HS metrics target_intervals->collect_roi_hs_metrics target_intervals reference reference collect_detailed_hs_metrics HS Metrics workflow reference->collect_detailed_hs_metrics reference collect_insert_size_metrics collect insert size metrics reference->collect_insert_size_metrics reference reference->select_variants reference collect_alignment_summary_metrics collect alignment summary metrics reference->collect_alignment_summary_metrics reference reference->collect_roi_hs_metrics reference bam bam verify_bam_id verify BAM ID bam->verify_bam_id bam bam->collect_detailed_hs_metrics bam bam->collect_insert_size_metrics bam bam->collect_alignment_summary_metrics bam bam->collect_roi_hs_metrics bam samtools_flagstat samtools flagstat bam->samtools_flagstat bam summary_intervals summary_intervals summary_intervals->collect_detailed_hs_metrics summary_intervals minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->collect_detailed_hs_metrics minimum_mapping_quality minimum_mapping_quality->collect_roi_hs_metrics minimum_mapping_quality minimum_base_quality minimum_base_quality minimum_base_quality->collect_detailed_hs_metrics minimum_base_quality minimum_base_quality->collect_roi_hs_metrics minimum_base_quality per_target_intervals per_target_intervals per_target_intervals->collect_detailed_hs_metrics per_target_intervals omni_vcf omni_vcf omni_vcf->select_variants vcf per_base_intervals per_base_intervals per_base_intervals->collect_detailed_hs_metrics per_base_intervals picard_metric_accumulation_level picard_metric_accumulation_level picard_metric_accumulation_level->collect_insert_size_metrics metric_accumulation_level picard_metric_accumulation_level->collect_alignment_summary_metrics metric_accumulation_level bait_intervals bait_intervals bait_intervals->collect_roi_hs_metrics bait_intervals per_base_coverage_metrics per_base_coverage_metrics flagstats flagstats hs_metrics hs_metrics insert_size_metrics insert_size_metrics per_target_hs_metrics per_target_hs_metrics verify_bam_id_metrics verify_bam_id_metrics per_base_hs_metrics per_base_hs_metrics summary_hs_metrics summary_hs_metrics per_target_coverage_metrics per_target_coverage_metrics verify_bam_id_depth verify_bam_id_depth alignment_summary_metrics alignment_summary_metrics insert_size_histogram insert_size_histogram verify_bam_id->verify_bam_id_metrics verify_bam_id->verify_bam_id_depth collect_detailed_hs_metrics->per_base_coverage_metrics collect_detailed_hs_metrics->per_target_hs_metrics collect_detailed_hs_metrics->per_base_hs_metrics collect_detailed_hs_metrics->summary_hs_metrics collect_detailed_hs_metrics->per_target_coverage_metrics collect_insert_size_metrics->insert_size_metrics collect_insert_size_metrics->insert_size_histogram select_variants->verify_bam_id vcf collect_alignment_summary_metrics->alignment_summary_metrics collect_roi_hs_metrics->hs_metrics samtools_flagstat->flagstats default1 false default1->collect_roi_hs_metrics per_target_coverage default2 false default2->collect_roi_hs_metrics per_base_coverage
Workflow as SVG
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  • Inputs/Outputs

Inputs

ID Type Title Doc
bam File
omni_vcf File
reference File
bait_intervals File
target_intervals File
summary_intervals https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/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
select_variants
../tools/select_variants.cwl (CommandLineTool)
SelectVariants (GATK 3.6)
samtools_flagstat
../tools/samtools_flagstat.cwl (CommandLineTool)
samtools flagstat
collect_roi_hs_metrics
../tools/collect_hs_metrics.cwl (CommandLineTool)
collect HS metrics
collect_detailed_hs_metrics
hs_metrics.cwl (Workflow)
HS Metrics workflow
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
hs_metrics File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
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Permalink: https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/subworkflows/qc_exome.cwl