nf-core_modules/software/bwameth/align/meta.yml

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name: bwameth_align
description: Performs alignment of BS-Seq reads using bwameth
keywords:
- bwameth
- alignment
- 3-letter genome
- map
- methylation
- 5mC
- methylseq
- bisulphite
- fastq
- bam
tools:
- bwameth:
description: |
Fast and accurate alignment of BS-Seq reads
using bwa-mem and a 3-letter genome.
homepage: https://github.com/brentp/bwa-meth
documentation: https://github.com/brentp/bwa-meth
arxiv: arXiv:1401.1129
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 ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- index:
type: dir
description: Directory containing bwameth genome index
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output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Output BAM file containing read alignments
pattern: "*.{bam}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@phue"