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/sequoia/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
disable_version_detection: true
report_section_order:
    kraken:
        order: -994
    NOWAYOUT_collated_table:
        order: -995
    NOWAYOUT_INDIV_READS_MAPPED_collated_table:
        order: -996
    fastp:
        order: -997
    fastqc:
        order: -998
    software_versions:
        order: -999

export_plots: true

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

module_order:
    - kraken:
          name: "SOURMASH TAX METAGENOME"
          href: "https://sourmash.readthedocs.io/en/latest/command-line.html#sourmash-tax-metagenome-summarize-metagenome-content-from-gather-results"
          doi: "10.21105/joss.00027"
          info: >
              section of the report shows how <b>reads</b> are approximately classified.
              Please note that the plot title below is shown as
              <b>Kraken2: Top taxa</b> since <code>kreport</code> fornat was used
              to create Kraken-style reports with <code>sourmash tax metagenome</code>.
          path_filters:
              - "*.kreport.txt"
    - fastqc:
          name: "FastQC"
          info: >
              section of the report shows FastQC results <b>before</b> adapter trimming
              on SE reads or on merged PE reads.
          path_filters:
              - "*_fastqc.zip"
    - 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 reads or on merged PE reads.
          path_filters:
              - "*.fastp.json"
