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

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
        licence: ['MIT']
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}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@phue"