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

export_plots: true

data_format: "yaml"

top_modules:
  - "fastqc":
      name: "FastQC: raw reads"
      path_filters_exclude:
        - "*trimmed*"
  - "fastp"
  - "adapterRemoval":
  - custom_content
  - "fastqc":
      name: "FastQC: after preprocessing"
      info: "After trimming and, if requested, contamination removal."
      path_filters:
        - "*trimmed*"
  - "busco":
      info: "assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs. In case BUSCO's automated lineage selection was used, only generic results for the selected domain are shown and only for genome bins and kept, unbinned contigs for which the BUSCO analysis was successfull, i.e. not for contigs for which no BUSCO genes could be found. Bins for which a specific virus lineage was selected are also not shown."
  - "quast"

custom_data:
  host_removal:
    file_format: "tsv"
    section_name: "Bowtie 2: host read removal"
    description: "Reads are mapped against the host reference sequence. Only reads that do not align (concordantly) are kept for further analysis."
    plot_type: "bargraph"
    pconfig:
      id: "host_removal_bargraph"
      title: "Bowtie 2: reads mapped against host reference"
      ylab: "# Reads"

sp:
  host_removal:
    fn: "host_removal_metrics.tsv"
  adapterRemoval:
    fn: "*_ar2_*.log"

extra_fn_clean_exts:
  - ".bowtie2"
  - "_ar2"
