Workflow: umi molecular alignment workflow

Fetched 2023-01-13 05:48:30 GMT
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Inputs

ID Type Title Doc
bam File[]
min_reads Integer[]
reference String
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
index_bam
../tools/index_bam.cwl (CommandLineTool)
samtools index
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_molecular_consensus
../tools/call_molecular_consensus.cwl (CommandLineTool)
call molecular 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/735be84cdea041fcc8bd8cbe5728b29ca3586a21/definitions/subworkflows/molecular_alignment.cwl