Workflow: WGS QC workflow

Fetched 2023-01-10 04:09:24 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs picard_metric_accumulation_level picard_metric_accumulation_level collect_alignment_summary_metrics collect alignment summary metrics picard_metric_accumulation_level->collect_alignment_summary_metrics metric_accumulation_level collect_gc_bias_metrics collect gc bias metrics picard_metric_accumulation_level->collect_gc_bias_metrics metric_accumulation_level collect_insert_size_metrics collect insert size metrics picard_metric_accumulation_level->collect_insert_size_metrics metric_accumulation_level intervals intervals collect_wgs_metrics collect WGS metrics intervals->collect_wgs_metrics intervals reference reference reference->collect_alignment_summary_metrics reference collect_hs_metrics HS Metrics workflow reference->collect_hs_metrics reference reference->collect_wgs_metrics reference reference->collect_gc_bias_metrics reference cgpbigwig_bamcoverage cgpBigWig Converting BAM to BigWig reference->cgpbigwig_bamcoverage reference reference->collect_insert_size_metrics reference per_target_intervals per_target_intervals per_target_intervals->collect_hs_metrics per_target_intervals bam bam bam->collect_alignment_summary_metrics bam bam->collect_hs_metrics bam bam->collect_wgs_metrics bam verify_bam_id verify BAM ID bam->verify_bam_id bam bam->collect_gc_bias_metrics bam bam->cgpbigwig_bamcoverage bam samtools_flagstat samtools flagstat bam->samtools_flagstat bam bam->collect_insert_size_metrics bam minimum_base_quality minimum_base_quality minimum_base_quality->collect_hs_metrics minimum_base_quality per_base_intervals per_base_intervals per_base_intervals->collect_hs_metrics per_base_intervals sample_name sample_name sample_name->collect_wgs_metrics sample_name sample_name->collect_gc_bias_metrics sample_name omni_vcf omni_vcf omni_vcf->verify_bam_id vcf summary_intervals summary_intervals summary_intervals->collect_hs_metrics summary_intervals minimum_mapping_quality minimum_mapping_quality minimum_mapping_quality->collect_hs_metrics minimum_mapping_quality gc_bias_metrics_chart gc_bias_metrics_chart flagstats flagstats gc_bias_metrics gc_bias_metrics per_base_hs_metrics per_base_hs_metrics per_base_coverage_metrics per_base_coverage_metrics bamcoverage_bigwig bamcoverage_bigwig insert_size_histogram insert_size_histogram wgs_metrics wgs_metrics alignment_summary_metrics alignment_summary_metrics insert_size_metrics insert_size_metrics verify_bam_id_metrics verify_bam_id_metrics verify_bam_id_depth verify_bam_id_depth per_target_coverage_metrics per_target_coverage_metrics per_target_hs_metrics per_target_hs_metrics gc_bias_metrics_summary gc_bias_metrics_summary summary_hs_metrics summary_hs_metrics collect_alignment_summary_metrics->alignment_summary_metrics collect_hs_metrics->per_base_hs_metrics collect_hs_metrics->per_base_coverage_metrics collect_hs_metrics->per_target_coverage_metrics collect_hs_metrics->per_target_hs_metrics collect_hs_metrics->summary_hs_metrics collect_wgs_metrics->wgs_metrics verify_bam_id->verify_bam_id_metrics verify_bam_id->verify_bam_id_depth collect_gc_bias_metrics->gc_bias_metrics_chart collect_gc_bias_metrics->gc_bias_metrics collect_gc_bias_metrics->gc_bias_metrics_summary cgpbigwig_bamcoverage->bamcoverage_bigwig samtools_flagstat->flagstats collect_insert_size_metrics->insert_size_histogram collect_insert_size_metrics->insert_size_metrics
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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/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/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
cgpbigwig_bamcoverage
../tools/bam_to_bigwig.cwl (CommandLineTool)
cgpBigWig Converting BAM to BigWig
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
bamcoverage_bigwig 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[]
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Permalink: https://w3id.org/cwl/view/git/7638b3075863ae8172f4adaec82fb2eb8e80d3d5/definitions/subworkflows/qc_wgs.cwl