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:
  "nf-core-taxprofiler-methods-description":
    order: -1000
  software_versions:
    order: -1001
  "nf-core-taxprofiler-summary":
    order: -1002

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
  - samtools
  - kraken
  - malt
  - custom_content

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

top_modules:
  - "fastqc":
      name: "FastQC (pre-Trimming)"
      path_filters:
        - "*raw_*fastqc.zip"
  - "fastp"
  - "adapterRemoval"
  - "fastqc":
      name: "FastQC (post-Trimming)"
      path_filters:
        - "*raw_*processed.zip"
  - "kraken":
      name: "Kraken"
      path_filters:
        - "*.kraken2.report.txt"
  - "kraken":
      name: "Centrifuge"
      anchor: "centrifuge"
      target: "Centrifuge"
      doi: "10.1101/gr.210641.116"
      info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title"
      extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
      path_filters:
        - "*.centrifuge.txt"