Workflow: umi molecular alignment workflow

Fetched 2023-01-05 07:03:00 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs reference reference filter_consensus filter consensus reads reference->filter_consensus reference align_consensus umi realignment reference->align_consensus reference align umi per-lane alignment subworkflow reference->align reference clip_overlap clip overlapping reads reference->clip_overlap reference read_structure read_structure read_structure->align read_structure bam bam bam->align bam max_read_error_rate max_read_error_rate max_read_error_rate->filter_consensus max_read_error_rate min_base_quality min_base_quality min_base_quality->filter_consensus min_base_quality sample_name sample_name collect_duplex_seq_metrics collect duplex seq metrics sample_name->collect_duplex_seq_metrics description min_reads min_reads min_reads->filter_consensus min_reads max_no_call_fraction max_no_call_fraction max_no_call_fraction->filter_consensus max_no_call_fraction target_intervals target_intervals target_intervals->collect_duplex_seq_metrics intervals max_base_error_rate max_base_error_rate max_base_error_rate->filter_consensus max_base_error_rate aligned_bam aligned_bam duplex_seq_metrics duplex_seq_metrics adapter_histogram adapter_histogram filter_consensus->clip_overlap bam align_consensus->filter_consensus bam index_bam samtools index index_bam->aligned_bam call_molecular_consensus call molecular consensus call_molecular_consensus->align_consensus bam group_reads_by_umi group reads by umi group_reads_by_umi->call_molecular_consensus bam group_reads_by_umi->collect_duplex_seq_metrics bam align->adapter_histogram merge Sambamba: merge align->merge bams collect_duplex_seq_metrics->duplex_seq_metrics merge->group_reads_by_umi bam clip_overlap->index_bam bam
Workflow as SVG
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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
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/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/subworkflows/molecular_alignment.cwl