From ba2eb7b705588974c19d5b9b06ec6b7fa0098545 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 18 Dec 2024 15:42:40 +0100
Subject: [PATCH] Blacklist some sections in the MultiQC report

To reduce the clutter in the report, we disable some sections that do
not contain a lot of relevant information.
---
 cfg/multiqc.yml      | 9 +++++++++
 test/test_hamlet.yml | 9 +++++++++
 2 files changed, 18 insertions(+)

diff --git a/cfg/multiqc.yml b/cfg/multiqc.yml
index d759a25..7892566 100644
--- a/cfg/multiqc.yml
+++ b/cfg/multiqc.yml
@@ -35,6 +35,15 @@ report_section_order:
   picard:
     order: 700
 
+remove_sections:
+  - sequali_sequence_duplication_levels
+  - sequali_top_overrepresented_sequences_read1
+  - sequali_top_overrepresented_sequences_read2
+  - sequali_adapter_content_from_overlap
+  - sift_summary
+  - polyphen_summary
+  - position_in_protein
+
 sample_names_replace_regex: True
 sample_names_replace:
   "(.+) \\| qc-seq \\| (.+).cutadapt.json": "\\1"
diff --git a/test/test_hamlet.yml b/test/test_hamlet.yml
index fffa597..9c54855 100644
--- a/test/test_hamlet.yml
+++ b/test/test_hamlet.yml
@@ -160,6 +160,15 @@
         - "Picard"
         # Custom MultiQC output from the expression module
         - "mqc_expression_unstranded"
+      # Blacklisted MultiQC sections
+      must_not_contain:
+        - "sequali_sequence_duplication_levels"
+        - "sequali_top_overrepresented_sequences_table_read1"
+        - "sequali_top_overrepresented_sequences_table_read2"
+        - "sift_summary"
+        - "polyphen_summary"
+        - "position_in_protein"
+        - "sequali_adapter_content_from_overlap"
     # Test that we remove the temporary folder from snv-indels
     - path: "snv-indel-tmp"
       should_exist: False