title: CPIPES Report
intro_text: >
    CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. 
report_comment: >
    This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/bettercallsal/blob/master/readme/Workflow_Name_Placeholder.md" target="_blank">CPIPES - Workflow_Name_Placeholder</a>
    analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
report_header_info:
    - CPIPES Version: CPIPES_Version_Placeholder
    - Workflow: Workflow_Name_Placeholder
    - Workflow Version: Workflow_Version_Placeholder
    - Conceived By: 'Kranti Konganti'
    - Input Directory: Workflow_Input_Placeholder
    - Output Directory: Workflow_Output_Placeholder
show_analysis_paths: False
show_analysis_time: False
report_section_order:
    BETTERCALLSAL_SALMON_COUNTS:
        order: -898
    BETTERCALLSAL_SALYN_collated_table:
        order: -899
    BETTERCALLSAL_collated_table:
        order: -900
    BCS_SOURMASH_MATRIX_collated_table:
        order: -991
    MLST_collated_table:
        order: -992
    ABRICATE_NCBIAMRPLUS_collated_table:
        order: -993
    ABRICATE_MEGARES_collated_table:
        order: -994
    ABRICATE_RESFINDER_collated_table:
        order: -995
    ABRICATE_ARGANNOT_collated_table:
        order: -996
    fastp:
        order: -997
    fastqc:
        order: -998
    software_versions:
        order: -999

export_plots: true

# Run only these modules
run_modules:
    - fastp
    - fastqc
    - custom_content

module_order:
    - fastp:
        name: 'fastp'
        info: >
            section of the report shows read statistics <b>before</b> and <b>after</b> adapter trimming
            with <code>fastp</code> on SE, merged PE or concatenated PE reads.
        path_filters:
            - '*.fastp.json'
    - fastqc:
        name: 'FastQC'
        info: >
            section of the report shows FastQC results <b>before</b> adapter trimming
            on SE, merged PE or concatenated PE reads.
        path_filters:
            - '*_fastqc.zip'