nf-core_modules/software/bismark/genome_preparation/meta.yml

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2021-02-18 09:56:36 +00:00
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"