Workflow: umi duplex alignment fastq workflow
Fetched 2023-01-11 19:49:12 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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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 |
|---|---|---|---|
| platform | String[] | ||
| reference | String | ||
| read1_fastq | File[] | ||
| read2_fastq | File[] | ||
| sample_name | String | ||
| library_name | String[] | ||
| platform_unit | String[] | ||
| read_structure | String[] | ||
| target_intervals | File (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastq_to_bam |
../tools/fastq_to_bam.cwl
(CommandLineTool)
|
fastq to bam | |
| alignment_workflow |
../subworkflows/duplex_alignment.cwl
(Workflow)
|
umi duplex alignment workflow |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| aligned_bam | File | ||
| adapter_histogram | File[] | ||
| duplex_seq_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/f45b52a24c7b54a75368dcbab24b4eb2c5a9c75a/definitions/pipelines/umi_duplex_alignment.cwl
