kkonganti@101: custom_logo: "FDa-Logo-Blue---medium-01.png"
kkonganti@101: custom_logo_url: "https://www.fda.gov/about-fda/fda-organization/center-food-safety-and-applied-nutrition-cfsan"
kkonganti@101: custom_logo_title: "CFSAN, FDA"
kkonganti@101: title: CPIPES Report
kkonganti@101: intro_text: >
kkonganti@101:     CPIPES (CFSAN PIPELINES) is a modular bioinformatics data analysis project at CFSAN, FDA based on NEXTFLOW DSL2. 
kkonganti@101: report_comment: >
kkonganti@101:     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>
kkonganti@101:     analysis pipeline. Only certain tables and plots are reported here. For complete results, please refer to the analysis pipeline output directory.
kkonganti@101: report_header_info:
kkonganti@101:     - CPIPES Version: CPIPES_Version_Placeholder
kkonganti@101:     - Workflow: Workflow_Name_Placeholder
kkonganti@101:     - Workflow Version: Workflow_Version_Placeholder
kkonganti@101:     - Input Directory: Workflow_Input_Placeholder
kkonganti@101:     - Output Directory: Workflow_Output_Placeholder
kkonganti@101:     - Developer E-mail: 'Kranti.Konganti@fda.hhs.gov'
kkonganti@101:     - Stakeholder E-mail: 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
kkonganti@101: show_analysis_paths: False
kkonganti@101: show_analysis_time: False
kkonganti@101: report_section_order:
kkonganti@101:     MLST_collated_table:
kkonganti@101:         order: -989
kkonganti@101:     ECTYPER_collated_table:
kkonganti@101:         order: -990
kkonganti@101:     SEROTYPEFINDER_collated_table:
kkonganti@101:         order: -991
kkonganti@101:     SEQSERO2_collated_table:
kkonganti@101:         order: -992
kkonganti@101:     ABRICATE_ECOLI_VF_collated_table:
kkonganti@101:         order: -993
kkonganti@101:     ABRICATE_NCBI_collated_table:
kkonganti@101:         order: -994
kkonganti@101:     ABRICATE_NCBIAMRPLUS_collated_table:
kkonganti@101:         order: -995
kkonganti@101:     ABRICATE_MEGARES_collated_table:
kkonganti@101:         order: -996
kkonganti@101:     ABRICATE_RESFINDER_collated_table:
kkonganti@101:         order: -997
kkonganti@101:     ABRICATE_ARGANNOT_collated_table:
kkonganti@101:         order: -998
kkonganti@101:     software_versions:
kkonganti@101:         order: -999
kkonganti@101: 
kkonganti@101: export_plots: true
kkonganti@101: 
kkonganti@101: # Run only these modules
kkonganti@101: run_modules:
kkonganti@101:     - fastqc
kkonganti@101:     - kraken
kkonganti@101:     - custom_content
kkonganti@101: 
kkonganti@101: module_order:
kkonganti@101:     - fastqc:
kkonganti@101:             name: 'FastQC'
kkonganti@101:             info: 'section of the report shows FastQC results <b>before</b> adapter trimming.'
kkonganti@101:             path_filters:
kkonganti@101:                 - '*_fastqc.zip'
kkonganti@101:     - kraken:
kkonganti@101:             name: 'Centrifuge'
kkonganti@101:             href: 'https://ccb.jhu.edu/software/centrifuge'
kkonganti@101:             doi: '10.1101/gr.210641.116'
kkonganti@101:             info: >
kkonganti@101:                 section of the report shows how <b>reads</b> are classified.
kkonganti@101:                 Please note that the plot title below is shown as
kkonganti@101:                 <b>Kraken2: Top taxa</b> since <code>centrifuge-kreport</code> was used
kkonganti@101:                 to create Kraken-style reports from centrifuge output files.
kkonganti@101:             path_filters:
kkonganti@101:                 - '*.kreport.txt'
kkonganti@101:     - kraken:
kkonganti@101:             name: 'Kraken2'
kkonganti@101:             info: 'section of the report shows how <b>assembled contigs</b> are classified.'
kkonganti@101:             path_filters:
kkonganti@101:                 - '*.report.txt'
kkonganti@101: 
kkonganti@101: extra_fn_clean_exts:
kkonganti@101:     - '.centrifuge.kreport'
kkonganti@101:     - '.report'
kkonganti@101: 
kkonganti@101: table_columns_visible:
kkonganti@101:     Kraken: False
kkonganti@101:     Kraken2: False
kkonganti@101:     Centrifuge: False