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

export_plots: true

custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
custom_logo_url: https://nf-co.re/taxprofiler
custom_logo_title: "nf-core/taxprofiler"

run_modules:
    - fastqc
    - adapterRemoval
    - fastp
    - bowtie2
    - kraken
    - malt

#extra_fn_clean_exts:
#    - '_fastp'
#    - '.pe.settings'
#    - '.se.settings'

top_modules:
  - 'fastqc':
    name: "FastQC (pre-processing)"
    path_filters:
      - '*_raw.zip'
  - 'fastp'
  - 'fastqc':
    name: "FastQC (post-processing)"
    path_filters:
      - '*_processed.zip'
  - 'kraken':
    name: "Kraken"
    path_filters:
      - '*kraken.report'
  - 'kraken':
    name: Centrifuge"
    path_filters:
      - '*centrifuge.kreport'