--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/conf/multiqc/nowayout_mqc.yml	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,65 @@
+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"