Merge branch 'reporting'

Author: nrminor

.gitignore

@@ -85,6 +85,19 @@
 !/bin/oneroof_cli/commands/
 !/bin/oneroof_cli/commands/*.py
 
+# reporting package (metrics extraction, visualization, report assembly)
+!/bin/reporting/
+!/bin/reporting/*.py
+!/bin/reporting/extractors/
+!/bin/reporting/extractors/*.py
+!/bin/reporting/visualizations/
+!/bin/reporting/visualizations/*.py
+
+# assets (templates, configs)
+!/assets/
+!/assets/*.yaml
+!/assets/*.yml
+
 # Rust development files for IDE support
 !/Cargo.toml
 !/Cargo.lock

assets/multiqc_config.yaml

@@ -0,0 +1,47 @@
+# MultiQC configuration for OneRoof reports
+# This file is used as a base template - dynamic values are substituted at runtime
+
+title: "OneRoof Amplicon Sequencing Report"
+subtitle: "Platform: {platform} | Reference: {reference}"
+
+# Report section order (negative = earlier)
+report_section_order:
+  oneroof_general_stats:
+    order: -1000
+  oneroof_coverage_table:
+    order: -900
+  software_versions:
+    order: -800
+
+# Search patterns for OneRoof custom content files
+sp:
+  oneroof_general_stats:
+    fn: "*_oneroof_general_stats.tsv"
+  oneroof_coverage_table:
+    fn: "*_oneroof_coverage_table.tsv"
+
+# Custom colors for QC status indicators
+custom_colours:
+  pass: "#22c55e"
+  warn: "#f59e0b"
+  fail: "#ef4444"
+
+# Table column visibility defaults
+table_columns_visible:
+  FastQC:
+    percent_duplicates: false
+    percent_gc: true
+    avg_sequence_length: true
+    percent_fails: false
+    total_sequences: true
+
+# Don't include these in the report
+exclude_modules:
+  - "snippy"
+
+# Clean up sample names
+fn_clean_exts:
+  - ".per-base"
+  - ".consensus"
+  - "_coverage_metrics"
+  - "_variant_effects"