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.
LUMC · Dec 18, 2024 · ba2eb7b · ba2eb7b
1 parent 515d241
commit ba2eb7b
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diff --git 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
@@ -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