Workflow: umi duplex alignment workflow

Fetched 2023-01-10 00:04:24 GMT
children parents
workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs reference reference clip_overlap clip overlapping reads reference->clip_overlap reference filter_consensus filter consensus reads reference->filter_consensus reference align umi per-lane alignment subworkflow reference->align reference align_consensus umi realignment reference->align_consensus reference read_structure read_structure read_structure->align read_structure target_intervals target_intervals collect_duplex_seq_metrics collect duplex seq metrics target_intervals->collect_duplex_seq_metrics intervals min_base_quality min_base_quality min_base_quality->filter_consensus min_base_quality max_no_call_fraction max_no_call_fraction max_no_call_fraction->filter_consensus max_no_call_fraction max_read_error_rate max_read_error_rate max_read_error_rate->filter_consensus max_read_error_rate min_reads min_reads min_reads->filter_consensus min_reads max_base_error_rate max_base_error_rate max_base_error_rate->filter_consensus max_base_error_rate sample_name sample_name sample_name->collect_duplex_seq_metrics description bam bam bam->align bam adapter_histogram adapter_histogram aligned_bam aligned_bam duplex_seq_metrics duplex_seq_metrics call_duplex_consensus call duplex consensus call_duplex_consensus->align_consensus bam clip_overlap->aligned_bam merge Sambamba: merge group_reads_by_umi group reads by umi merge->group_reads_by_umi bam filter_consensus->clip_overlap bam group_reads_by_umi->call_duplex_consensus bam group_reads_by_umi->collect_duplex_seq_metrics bam collect_duplex_seq_metrics->duplex_seq_metrics align->adapter_histogram align->merge bams align_consensus->filter_consensus bam
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
bam File[]
min_reads Integer[]
reference File
sample_name String
read_structure String[]
min_base_quality Integer
target_intervals File (Optional)
max_base_error_rate Float (Optional)
max_read_error_rate Float (Optional)
max_no_call_fraction Float

Steps

ID Runs Label Doc
align
umi_alignment.cwl (Workflow)
umi per-lane alignment subworkflow
merge
../tools/merge_bams.cwl (CommandLineTool)
Sambamba: merge
clip_overlap
../tools/clip_overlap.cwl (CommandLineTool)
clip overlapping reads
align_consensus
../tools/realign.cwl (CommandLineTool)
umi realignment
filter_consensus
../tools/filter_consensus.cwl (CommandLineTool)
filter consensus reads
group_reads_by_umi
../tools/group_reads.cwl (CommandLineTool)
group reads by umi
call_duplex_consensus
../tools/call_duplex_consensus.cwl (CommandLineTool)
call duplex consensus
collect_duplex_seq_metrics
../tools/duplex_seq_metrics.cwl (CommandLineTool)
collect duplex seq metrics

Outputs

ID Type Label Doc
aligned_bam File
adapter_histogram File[]
duplex_seq_metrics File[]
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/subworkflows/duplex_alignment.cwl