Workflow: Raw sequence data to BQSR

Fetched 2023-01-10 21:42:41 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
trimming https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File
unaligned https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/definitions/types/sequence_data.yml#sequence_data[]
final_name String
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.

Steps

ID Runs Label Doc
bqsr
../tools/bqsr.cwl (CommandLineTool)
create BQSR table
align adapter for sequence_align_and_tag

Some workflow engines won't stage files in our nested structure, so parse it out here

merge
../tools/merge_bams.cwl (CommandLineTool)
Sambamba: merge
index_bam
../tools/index_bam.cwl (CommandLineTool)
samtools index
name_sort
../tools/name_sort.cwl (CommandLineTool)
sort BAM by name
apply_bqsr
../tools/apply_bqsr.cwl (CommandLineTool)
apply BQSR
mark_duplicates_and_sort
../tools/mark_duplicates_and_sort.cwl (CommandLineTool)
Mark duplicates and Sort

Outputs

ID Type Label Doc
final_bam File
mark_duplicates_metrics_file File
Permalink: https://w3id.org/cwl/view/git/174f3b239018328cec1d821947438b457552724c/definitions/subworkflows/sequence_to_bqsr.cwl