nf-core_modules/modules/bismark/summary/meta.yml

name: bismark_summary
description: |
    Uses Bismark report files of several samples in a run folder
    to generate a graphical summary HTML report.
keywords:
    - bismark
    - qc
    - methylation
    - 5mC
    - methylseq
    - bisulphite
    - report
    - summary
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
        licence: ['GPL-3.0-or-later']
input:
    - bam:
        type: file
        description: Bismark alignment
        pattern: "*.{bam}"
    - align_report:
        type: file
        description: Bismark alignment reports
        pattern: "*{report.txt}"
    - dedup_report:
        type: file
        description: Bismark deduplication reports
        pattern: "*.{deduplication_report.txt}"
    - splitting_report:
        type: file
        description: Bismark splitting reports
        pattern: "*{splitting_report.txt}"
    - mbias:
        type: file
        description: Text file containing methylation bias information
        pattern: "*.{txt}"
output:
    - summary:
        type: file
        description: Bismark summary
        pattern: "*.{html,txt}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@phue"