report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/2.5.0"
  target="_blank">nf-core/bacass</a> analysis pipeline. For information about how
  to interpret these results, please see the <a href="https://nf-co.re/bacass/2.5.0/docs/output"
  target="_blank">documentation</a>.

max_table_rows: 10000

module_order:
  - fastqc:
      name: "PREPROCESS: FastQC (raw reads)"
      info: "This section of the report shows FastQC results for the raw reads before
        adapter trimming."
      path_filters:
        - "./fastqc/*.zip"
  - fastqc:
      name: "PREPROCESS: FastQC (trimmed reads)"
      info: "This section of the report shows FastQC results for the processed and trimmed
        reads."
      path_filters:
        - "./fastqc_trim/*.zip"
  - fastp:
      name: "PREPROCESS: fastp (adapter trimming)"
      info: "This section of the report shows fastp results for reads after adapter
        and quality trimming."
      path_filters:
        - "./fastp/*.json"

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

export_plots: true

disable_version_detection: true
use_filename_as_sample_name:
  - prokka
  - bakta
