mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
59 lines
1.9 KiB
YAML
59 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"
|