custom_logo: "FDa-Logo-Blue---medium-01.png"
custom_logo_url: "https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan"
custom_logo_title: "CFSAN, FDA"
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://cfsan-git.fda.gov/Kranti.Konganti/cpipes/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
    - Input Directory: Workflow_Input_Placeholder
    - Output Directory: Workflow_Output_Placeholder
    - Developer E-mail: 'Kranti.Konganti@fda.hhs.gov'
    - Stakeholder E-mail: 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
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