--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/conf/multiqc/cronology_mqc.yml	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,68 @@
+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/cronology/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
+report_section_order:
+    MLST_collated_table:
+        order: -989
+    RMLST_collated_table:
+        order: -990
+    prokka:
+        order: -991
+    quast:
+        order: -992
+    ABRICATE_NCBIAMRPLUS_collated_table:
+        order: -993
+    ABRICATE_MEGARES_collated_table:
+        order: -994
+    ABRICATE_RESFINDER_collated_table:
+        order: -995
+    ABRICATE_ARGANNOT_collated_table:
+        order: -996
+    fastp:
+        order: -997
+    fastqc:
+        order: -998
+    software_versions:
+        order: -999
+
+export_plots: true
+
+# Run only these modules
+run_modules:
+    - fastp
+    - fastqc
+    - prokka
+    - quast
+    - custom_content
+
+module_order:
+    - 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, merged PE or concatenated PE reads.
+        path_filters:
+            - '*.fastp.json'
+    - fastqc:
+        name: 'FastQC'
+        info: >
+            section of the report shows FastQC results <b>before</b> adapter trimming
+            on SE, merged PE or concatenated PE reads.
+        path_filters:
+            - '*_fastqc.zip'
+
+# Custom module config
+prokka_table: true
+