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

export_plots: true

data_format: 'yaml'

max_table_rows: 10000

run_modules:
    - custom_content
    - fastp
    - samtools
    - bcftools

module_order:
    - fastp:
        name: 'PREPROCESS: fastp (adapter trimming)'
        info: 'This section of the report shows fastp results for reads after adapter and quality trimming.'
    - samtools:
        name: 'MAPPING: SAMTools (raw)'
        anchor: 'samtools'
        info: 'This section of the report shows SAMTools counts/statistics after mapping with BWA.'
        path_filters:
            - './samtools/*'
    - bcftools:
        name: 'VARIANTS: BCFTools (BCFTools)'
        anchor: 'bcftools'
        info: 'This section of the report shows BCFTools stats results for variants called by BCFTools.'
        path_filters:
            - './variants/*.txt'
