--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/conf/multiqc/bettercallsal_lr_mqc.yml	Thu May 28 20:41:10 2026 +0000
@@ -0,0 +1,75 @@
+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/bettercallsal/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
+skip_versions_section: True
+disable_version_detection: true
+report_section_order:
+    BETTERCALLSAL_SALMON_COUNTS:
+        order: -897
+    BETTERCALLSAL_SALYN_collated_table:
+        order: -898
+    BETTERCALLSAL_collated_table:
+        order: -899
+    BCS_SOURMASH_MATRIX_collated_table:
+        order: -900
+    MLST_collated_table:
+        order: -991
+    ABRICATE_NCBIAMRPLUS_collated_table:
+        order: -992
+    ABRICATE_MEGARES_collated_table:
+        order: -993
+    ABRICATE_RESFINDER_collated_table:
+        order: -994
+    ABRICATE_ARGANNOT_collated_table:
+        order: -995
+    filtlong:
+        order: -996
+    fastqc:
+        order: -997
+    fastqc-1:
+        order: -998
+    software_versions:
+        order: -999
+
+export_plots: true
+
+# Run only these modules
+run_modules:
+    - filtlong
+    - fastqc
+    - custom_content
+
+module_order:
+    - filtlong:
+          name: "filtlong"
+          info: >
+              section of the report shows read statistics <b>before</b> and <b>after</b> quality trimming
+              with <code>filtlong</code> on raw long reads.
+          path_filters:
+              - "*.filtlong.log"
+    - fastqc:
+          name: "FastQC (Raw reads)"
+          info: >
+              section of the report shows FastQC results <b>before</b> quality control
+              on long reads.
+          path_filters:
+              - "*.raw_fastqc.zip"
+    - fastqc:
+          name: "FastQC (Filtered reads)"
+          info: >
+              section of the report shows FastQC results <b>after</b> quality control
+              on long reads.
+          path_filters:
+              - "*.filtered_fastqc.zip"