--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/conf/multiqc/centriflaken_hy_mqc.yml	Fri May 29 13:27:47 2026 +0000
@@ -0,0 +1,82 @@
+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 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://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