title: CPIPES Report
intro_text: >
    CPIPES is a modular bioinformatics data analysis project at HFP, FDA based on NEXTFLOW DSL2.
report_comment: >
    This report has been generated by the <a href="https://github.com/CFSAN-Biostatistics/centriflaken" 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
    - Input Directory: Workflow_Input_Placeholder
    - Output Directory: Workflow_Output_Placeholder
show_analysis_paths: False
show_analysis_time: False
report_section_order:
    MLST_collated_table:
        order: -989
    ECTYPER_collated_table:
        order: -990
    SEROTYPEFINDER_collated_table:
        order: -991
    SEQSERO2_collated_table:
        order: -992
    ABRICATE_ECOLI_VF_collated_table:
        order: -993
    ABRICATE_NCBI_collated_table:
        order: -994
    ABRICATE_NCBIAMRPLUS_collated_table:
        order: -995
    ABRICATE_MEGARES_collated_table:
        order: -996
    ABRICATE_RESFINDER_collated_table:
        order: -997
    ABRICATE_ARGANNOT_collated_table:
        order: -998
    software_versions:
        order: -999

export_plots: true

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

module_order:
    - fastqc:
          name: "FastQC"
          info: "section of the report shows FastQC results <b>before</b> adapter trimming."
          path_filters:
              - "*_fastqc.zip"
    - kraken:
          name: "Centrifuge"
          href: "https://ccb.jhu.edu/software/centrifuge"
          doi: "10.1101/gr.210641.116"
          info: >
              section of the report shows how <b>reads</b> are classified.
              Please note that the plot title below is shown as
              <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
              to create Kraken-style reports from centrifuge output files.
          path_filters:
              - "*.kreport.txt"
    - kraken:
          name: "Kraken2"
          info: "section of the report shows how <b>assembled contigs</b> are classified."
          path_filters:
              - "*.report.txt"

extra_fn_clean_exts:
    - ".centrifuge.kreport"
    - ".report"

table_columns_visible:
    Kraken: False
    Kraken2: False
    Centrifuge: False