custom_logo: ../../../docs/images/nf-core_sarek_logo.png
custom_logo_url: https://github.com/nf-core/sarek/
custom_logo_title: 'nf-core/sarek'

report_comment: >
    This report has been generated by the <a href="https://github.com/nf-core/sarek" target="_blank">nf-core/sarek</a>
    analysis pipeline. For information about how to interpret these results, please see the
    <a href="https://github.com/nf-core/sarek" target="_blank">documentation</a>.
report_section_order:
    software_versions:
        order: -1000
    nf-core-sarek-summary:
        order: -1001

export_plots: true

top_modules:
- 'fastqc':
     name: 'FastQC'
     path_filters_exclude: 
        - '*trimmed_fastqc*'
- 'fastqc':
     name: 'FastQC after trimming'
     info: 'FastQC after applying TrimGalore.'
     path_filters: 
        - '*trimmed_fastqc*'
- 'picard'
- 'gatk'
- 'samtools'
- 'qualimap'
- 'bcftools'
- 'vcftools'
- 'snpeff'