Workflow: umi per-lane alignment subworkflow
Fetched 2023-01-14 17:20:15 GMT
Verified with cwltool version 3.1.20221201130942
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| bam | File | ||
| reference | File | ||
| read_structure | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| align |
../tools/umi_align.cwl
(CommandLineTool)
|
umi alignment | |
| extract_umis |
../tools/extract_umis.cwl
(CommandLineTool)
|
extract umis from bam | |
| mark_illumina_adapters |
../tools/mark_illumina_adapters.cwl
(CommandLineTool)
|
fastq to bam |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| aligned_bam | File | ||
| adapter_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/ac87e0584685fe04e4010ecd77ae4f055f21d788/definitions/subworkflows/umi_alignment.cwl
