mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
60 lines
1.9 KiB
YAML
60 lines
1.9 KiB
YAML
|
name: fgbio_groupreadsbyumi
|
|||
|
|
description: |
|
|||
|
|
Groups reads together that appear to have come from the same original molecule.
|
|||
|
|
Reads are grouped by template, and then templates are sorted by the 5’ mapping positions
|
|||
|
|
of the reads from the template, used from earliest mapping position to latest.
|
|||
|
|
Reads that have the same end positions are then sub-grouped by UMI sequence.
|
|||
|
|
(!) Note: the MQ tag is required on reads with mapped mates (!)
|
|||
|
|
This can be added using samblaster with the optional argument --addMateTags.
|
|||
|
|
keywords:
|
|||
|
|
- UMI
|
|||
|
|
- groupreads
|
|||
|
|
- fgbio
|
|||
|
|
tools:
|
|||
|
|
- fgbio:
|
|||
|
|
description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
|
|||
|
|
homepage: http://fulcrumgenomics.github.io/fgbio/
|
|||
|
|
documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
|
|||
|
|
tool_dev_url: https://github.com/fulcrumgenomics/fgbio
|
|||
|
|
doi: ""
|
|||
|
|
licence: ['MIT']
|
|||
|
|
|
|||
|
|
input:
|
|||
|
|
- meta:
|
|||
|
|
type: map
|
|||
|
|
description: |
|
|||
|
|
Groovy Map containing sample information
|
|||
|
|
e.g. [ id:'test', single_end:false ]
|
|||
|
|
- bam:
|
|||
|
|
type: file
|
|||
|
|
description: |
|
|||
|
|
BAM file. Note: the MQ tag is required on reads with mapped mates (!)
|
|||
|
|
pattern: "*.bam"
|
|||
|
|
- strategy:
|
|||
|
|
type: value
|
|||
|
|
description: |
|
|||
|
|
Reguired argument: defines the UMI assignment strategy.
|
|||
|
|
Must be chosen among: Identity, Edit, Adjacency, Paired.
|
|||
|
|
|
|||
|
|
output:
|
|||
|
|
- meta:
|
|||
|
|
type: map
|
|||
|
|
description: |
|
|||
|
|
Groovy Map containing sample information
|
|||
|
|
e.g. [ id:'test', single_end:false ]
|
|||
|
|
- versions:
|
|||
|
|
type: file
|
|||
|
|
description: File containing software versions
|
|||
|
|
pattern: "versions.yml"
|
|||
|
|
- bam:
|
|||
|
|
type: file
|
|||
|
|
description: UMI-grouped BAM
|
|||
|
|
pattern: "*.bam"
|
|||
|
|
- histogram:
|
|||
|
|
type: file
|
|||
|
|
description: A text file containing the tag family size counts
|
|||
|
|
pattern: "*.txt"
|
|||
|
|
|
|||
|
|
authors:
|
|||
|
|
- "@lescai"
|