-
Notifications
You must be signed in to change notification settings - Fork 57
pipelines_alignment_umi_duplex.cwl
Travis CI User edited this page Feb 9, 2021
·
19 revisions
This page is auto-generated. Do not edit.
umi duplex alignment fastq workflow
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| sequence | sequence: sequencing data and readgroup information | sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required for FASTQs. For BAMs, this pipeline assumes that the RG information is already in the header. | ../types/sequence_data.yml#sequence_data[] | |
| sample_name | string | |||
| read_structure | string[] | |||
| reference | ['string', 'File'] | ['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa'] | ||
| target_intervals | File? |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| aligned_bam | File | ['^.bai'] | ||
| adapter_histogram | File[] | |||
| duplex_seq_metrics | File[] |
| Name | CWL Run |
|---|---|
| sequence_to_bam | tools/sequence_to_bam.cwl |
| alignment_workflow | subworkflows/duplex_alignment.cwl |