mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
58 lines
1.8 KiB
YAML
58 lines
1.8 KiB
YAML
|
name: bismark_genome_preparation
|
||
|
|
description: |
|
||
|
|
Converts a specified reference genome into two different bisulfite
|
||
|
|
converted versions and indexes them for alignments.
|
||
|
|
keywords:
|
||
|
|
- bismark
|
||
|
|
- 3-letter genome
|
||
|
|
- index
|
||
|
|
- methylation
|
||
|
|
- 5mC
|
||
|
|
- methylseq
|
||
|
|
- bisulphite
|
||
|
|
- fasta
|
||
|
|
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:
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: Input genome fasta file
|
||
|
|
output:
|
||
|
|
- index:
|
||
|
|
type: dir
|
||
|
|
description: Bismark genome index directory
|
||
|
|
pattern: "BismarkIndex"
|
||
|
|
- version:
|
||
|
|
type: file
|
||
|
|
description: File containing software version
|
||
|
|
pattern: "*.{version.txt}"
|
||
|
|
authors:
|
||
|
|
- "@phue"
|