Workflow: exome alignment with qc, no bqsr, no verify_bam_id

Fetched 2023-01-03 23:30:50 GMT
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Inputs

ID Type Title Doc
bams File[]
reference File
final_name String (Optional)
readgroups String[]
bait_intervals File
target_intervals File
summary_intervals https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/labelled_file.yml#labelled_file[]
per_target_intervals https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/types/labelled_file.yml#labelled_file[]
qc_minimum_base_quality Integer (Optional)
qc_minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
qc Exome QC workflow
alignment Unaligned bam to sorted, markduped bam

Outputs

ID Type Label Doc
bam File
flagstats File
hs_metrics File
summary_hs_metrics File[]
insert_size_metrics File
per_base_hs_metrics File[]
insert_size_histogram File
per_target_hs_metrics File[]
mark_duplicates_metrics File
alignment_summary_metrics File
per_base_coverage_metrics File[]
per_target_coverage_metrics File[]
Permalink: https://w3id.org/cwl/view/git/04d21c33a5f2950e86db285fa0a32a6659198d8a/definitions/pipelines/alignment_exome_nonhuman.cwl