Workflow: wgs alignment with qc

Fetched 2023-01-11 06:33:01 GMT
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Inputs

ID Type Title Doc
omni_vcf File
sequence https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/sequence_data.yml#sequence_data[] sequence: sequencing data and readgroup information

sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.

trimming https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/trimming_options.yml#trimming_options (Optional)
intervals File
reference File
sample_name String (Optional)
bqsr_intervals String[] (Optional)
bqsr_known_sites File[]

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

summary_intervals https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/labelled_file.yml#labelled_file[]
per_base_intervals https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/labelled_file.yml#labelled_file[]
minimum_base_quality Integer (Optional)
per_target_intervals https://w3id.org/cwl/view/git/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/types/labelled_file.yml#labelled_file[]
minimum_mapping_quality Integer (Optional)
picard_metric_accumulation_level String

Steps

ID Runs Label Doc
qc WGS QC workflow
alignment Raw sequence data to BQSR

Outputs

ID Type Label Doc
bam File
flagstats File
wgs_metrics File
gc_bias_metrics 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
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/35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a/definitions/pipelines/alignment_wgs.cwl