Workflow: bam_qc_stats

Fetched 2023-01-10 06:46:18 GMT
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Inputs

ID Type Title Doc
input File[]
reference File
bait_intervals File
target_intervals File
temporary_directory String (Optional)
hsmetrics_coverage_cap Integer (Optional) hsmetrics_coverage_cap
hsmetrics_minimum_base_quality Integer (Optional) hsmetrics_minimum_base_quality
hsmetrics_minimum_mapping_quality Integer (Optional) hsmetrics_minimum_mapping_quality

Steps

ID Runs Label Doc
gatk_collect_hs_metrics_4_1_8_0
access_qc__packed.cwl#gatk_collect_hs_metrics_4.1.8.0.cwl (CommandLineTool)
GATK-CollectHsMetrics
gatk_collect_insert_size_metrics_4_1_8_0
access_qc__packed.cwl#gatk_collect_insert_size_metrics_4.1.8.0.cwl (CommandLineTool)
GATK-CollectInsertSizeMetrics
gatk_collect_alignment_summary_metrics_4_1_3_0
access_qc__packed.cwl#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl (CommandLineTool)
GATK-CollectAlignmentSummaryMetrics

Outputs

ID Type Label Doc
gatk_collect_hs_metrics_txt File[]
gatk_collect_insert_size_metrics_txt File[]
gatk_collect_alignment_summary_metrics_txt File[]
gatk_collect_hs_metrics_per_base_coverage_txt File[]
gatk_collect_insert_size_metrics_histogram_pdf File[]
gatk_collect_hs_metrics_per_target_coverage_txt File[]
Permalink: https://w3id.org/cwl/view/git/248e7c3edaff48e1b97a7931d66aa3b23ce97f54/access_qc__packed.cwl?part=bam_qc_stats.cwl