# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: MultiQC
description: Aggregate results from bioinformatics analyses across many samples into a single report
keywords:
  - QC
  - bioinformatics tools
  - Beautiful stand-alone HTML report
tools:
  - multiqc:
      description: |
        MultiQC searches a given directory for analysis logs and compiles a HTML report.
        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
      homepage: https://multiqc.info/
      documentation: https://multiqc.info/docs/
      licence: ["GPL-3.0-or-later"]

input:
  - multiqc_files:
      type: file
      description: |
        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
  - multiqc_config:
      type: file
      description: Optional config yml for MultiQC
      pattern: "*.{yml,yaml}"
  - extra_multiqc_config:
      type: file
      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
      pattern: "*.{yml,yaml}"
  - multiqc_logo:
      type: file
      description: Optional logo file for MultiQC
      pattern: "*.{png}"

output:
  - report:
      type: file
      description: MultiQC report file
      pattern: "multiqc_report.html"
  - data:
      type: directory
      description: MultiQC data dir
      pattern: "multiqc_data"
  - plots:
      type: file
      description: Plots created by MultiQC
      pattern: "*_data"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@abhi18av"
  - "@bunop"
  - "@drpatelh"
  - "@jfy133"