Workflow: Raw sequence data to BQSR

Fetched 2023-06-06 09:11:53 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
trimming https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/types/trimming_options.yml#trimming_options (Optional)
reference File
unaligned https://w3id.org/cwl/view/git/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/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/bfcb5ffbea3d00a38cc03595d41e53ea976d599d/definitions/subworkflows/sequence_to_bqsr.cwl