mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
72 lines
2.3 KiB
YAML
72 lines
2.3 KiB
YAML
name: bismark_deduplicate
|
|
description: |
|
|
Removes alignments to the same position in the genome
|
|
from the Bismark mapping output.
|
|
keywords:
|
|
- bismark
|
|
- 3-letter genome
|
|
- map
|
|
- methylation
|
|
- 5mC
|
|
- methylseq
|
|
- bisulphite
|
|
- bam
|
|
tools:
|
|
- bismark:
|
|
description: |
|
|
Bismark is a tool to map bisulfite treated sequencing reads
|
|
and perform methylation calling in a quick and easy-to-use fashion.
|
|
homepage: https://github.com/FelixKrueger/Bismark
|
|
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
|
doi: 10.1093/bioinformatics/btr167
|
|
params:
|
|
- outdir:
|
|
type: string
|
|
description: |
|
|
The pipeline's output directory. By default, the module will
|
|
output files into `$params.outdir/<SOFTWARE>`
|
|
- publish_dir_mode:
|
|
type: string
|
|
description: |
|
|
Value for the Nextflow `publishDir` mode parameter.
|
|
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
|
- enable_conda:
|
|
type: boolean
|
|
description: |
|
|
Run the module with Conda using the software specified
|
|
via the `conda` directive
|
|
- singularity_pull_docker_container:
|
|
type: boolean
|
|
description: |
|
|
Instead of directly downloading Singularity images for use with Singularity,
|
|
force the workflow to pull and convert Docker containers instead.
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: BAM file containing read alignments
|
|
pattern: "*.{bam}"
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: Deduplicated output BAM file containing read alignments
|
|
pattern: "*.{deduplicated.bam}"
|
|
- report:
|
|
type: file
|
|
description: Bismark deduplication reports
|
|
pattern: "*.{deduplication_report.txt}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@phue"
|