subworkflows_umi_alignment.cwl - genome/analysis-workflows GitHub Wiki
Documentation for umi_alignment.cwl
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Overview
umi per-lane alignment subworkflow
Inputs
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| bam | File | |||
| read_structure | string[] | |||
| reference | ['string', 'File'] | ['.amb', '.ann', '.bwt', '.pac', '.sa'] |
Outputs
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| aligned_bam | File | ['^.bai'] | ||
| adapter_metrics | File |
Steps
| Name | CWL Run |
|---|---|
| extract_umis | tools/extract_umis.cwl |
| mark_illumina_adapters | tools/mark_illumina_adapters.cwl |
| align | tools/umi_align.cwl |