nf-core_modules/software/methyldackel/extract/meta.yml

78 lines
2.3 KiB
YAML

name: methyldackel_extract
description: Extracts per-base methylation metrics from alignments
keywords:
- methylation
- 5mC
- methylseq
- bisulphite
- consensus
- bedGraph
- bam
- cram
tools:
- methyldackel:
description: |
A (mostly) universal methylation extractor
for BS-seq experiments.
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 ]
- fasta:
type: file
description: Input genome fasta file
pattern: "*.{fasta,fa}"
- fai:
type: file
description: FASTA index file
pattern: "*.{fai}"
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- bai:
type: file
description: BAM/CRAM index file
pattern: "*.{bai,crai}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedgraph:
type: file
description: bedGraph file containing per-base methylation metrics
pattern: "*.{bedGraph}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@phue"