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
skip_versions_section: True
disable_version_detection: true
report_section_order:
    BETTERCALLSAL_SALMON_COUNTS:
        order: -897
    BETTERCALLSAL_SALYN_collated_table:
        order: -898
    BETTERCALLSAL_collated_table:
        order: -899
    BCS_SOURMASH_MATRIX_collated_table:
        order: -900
    MLST_collated_table:
        order: -991
    ABRICATE_NCBIAMRPLUS_collated_table:
        order: -992
    ABRICATE_MEGARES_collated_table:
        order: -993
    ABRICATE_RESFINDER_collated_table:
        order: -994
    ABRICATE_ARGANNOT_collated_table:
        order: -995
    filtlong:
        order: -996
    fastqc:
        order: -997
    fastqc-1:
        order: -998
    software_versions:
        order: -999

export_plots: true

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

module_order:
    - filtlong:
          name: "filtlong"
          info: >
              section of the report shows read statistics <b>before</b> and <b>after</b> quality trimming
              with <code>filtlong</code> on raw long reads.
          path_filters:
              - "*.filtlong.log"
    - fastqc:
          name: "FastQC (Raw reads)"
          info: >
              section of the report shows FastQC results <b>before</b> quality control
              on long reads.
          path_filters:
              - "*.raw_fastqc.zip"
    - fastqc:
          name: "FastQC (Filtered reads)"
          info: >
              section of the report shows FastQC results <b>after</b> quality control
              on long reads.
          path_filters:
              - "*.filtered_fastqc.zip"