MultiQC module

This module allow to run MultiQC on Eoulsan step output to generate a quality control report in HTML.

  • Internal name: multiqc
  • Available: Both local and distributed mode

  • Input port:
    • input1: FastQC report (format: fastqc_report_zip) if fastqc report is enabled
    • input2: Mapper log (format: mapper_results_log) if mapreads report is enabled
    • input3: Expression output (format: expression_results_tsv) if expression report is enabled

  • Output port:
    • output: report in HTML format (format: multiqc_report_html)

  • Optional parameters:
  • Parameter Type Description Default value
    reports string Define the reports to generate. The available reports are listed in the following table. Several reports can be generated by separating their names with comma fastqc
    use.docker boolean Enable Docker usage to execute MultiQC false
    docker.image string The docker image to use when Docker is enabled ewels/multiqc:v1.7

  • This module currently support the following reports:
  • Eoulsan report name MultiQC section name Note
    fastqc FastQC
    mapreads The MultiQC section name change against the mapper used in the workflow (e.g. Bowtie 1/Bowtie 2/STAR...) Warning: this report is not available in Hadoop mode.
    expression HTSeq Count
    featurecounts FeaturesCounts

  • Configuration example:
  • <!-- MultiQC step -->
    <step id="mymultiqcstep" skip="false" discardoutput="false">