Workflow: exome alignment with qc

Fetched 2022-10-03 01:21:10 GMT
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Inputs

ID Type Title Doc
bams File[]
mills File
omni_vcf File
dbsnp_vcf File
reference String
final_name String (Optional)
readgroups String[]
known_indels File
bait_intervals File
bqsr_intervals String[] (Optional)
target_intervals File
summary_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/types/labelled_file.yml#labelled_file[]
per_target_intervals https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/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 BQSR and VCF

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[]
verify_bam_id_depth File
insert_size_histogram File
per_target_hs_metrics File[]
verify_bam_id_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/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/pipelines/exome_alignment.cwl