diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
index 5d07c929..9416fbf1 100755
--- a/assets/multiqc_config.yaml
+++ b/assets/multiqc_config.yaml
@@ -20,100 +20,98 @@ exclude_modules:
 
 module_order:
     - fastqc:
-        name: 'FastQC (library; raw)'
-        info: 'This section of the report shows FastQC results before adapter trimming.'
+        name: 'LIB: FastQC (raw)'
+        info: 'This section of the report shows FastQC results before adapter trimming for individual libraries.'
         path_filters:
-            - '*_fastqc.zip'
-        path_filters_exclude:
-            - '*val*_fastqc.zip'
-            - '*trimmed_fastqc.zip'
+            - './fastqc/*.zip'
     - cutadapt:
-        name: 'cutadapt (library; trimmed)'
-        info: 'This section of the report shows the length of trimmed reads by cutadapt.'
-        path_filters:
-            - '*_trimming_report.txt'
+        name: 'LIB: Cutadapt (trimmed)'
+        info: 'This section of the report shows the length of trimmed reads by Cutadapt for individual libraries.'
     - fastqc:
-        name: 'FastQC (library; trimmed)'
-        info: 'This section of the report shows FastQC results after adapter trimming.'
+        name: 'LIB: FastQC (trimmed)'
+        info: 'This section of the report shows FastQC results after adapter trimming for individual libraries.'
         path_filters:
-            - '*val*_fastqc.zip'
-            - '*trimmed_fastqc.zip'
+            - './trimgalore/fastqc/*.zip'
     - samtools:
-        name: 'SAMTools (library)'
+        name: 'LIB: SAMTools'
         info: 'This section of the report shows SAMTools results for individual libraries.'
         path_filters:
-            - '*.Lb.sorted.bam*'
+            - './alignment/library/*'
     - samtools:
-        name: 'SAMTools (merged library; unfiltered)'
+        name: 'MERGED LIB: SAMTools (unfiltered)'
         info: 'This section of the report shows SAMTools results after merging libraries and before filtering.'
         path_filters:
-            - '*mLb.mkD.sorted.bam*'
+            - './alignment/mergedLibrary/*.mLb.mkD.sorted.bam*'
     - preseq:
-        name: 'Preseq (merged library; unfiltered)'
+        name: 'MERGED LIB: Preseq (unfiltered)'
         info: 'This section of the report shows Preseq results after merging libraries and before filtering.'
-        path_filters:
-            - '*mLb*'
     - samtools:
-        name: 'SAMTools (merged library; filtered)'
+        name: 'MERGED LIB: SAMTools (filtered)'
         info: 'This section of the report shows SAMTools results after merging libraries and after filtering.'
         path_filters:
-            - '*mLb.clN.sorted.bam*'
+            - './alignment/mergedLibrary/*.mLb.clN.sorted.bam*'
     - picard:
-        name: 'Picard (merged library; filtered)'
+        name: 'MERGED LIB: Picard'
         info: 'This section of the report shows picard results after merging libraries and after filtering.'
         path_filters:
-            - '*mLb*'
+            - './alignment/mergedLibrary/picard_metrics/*'
     - deeptools:
-        name: 'deepTools'
+        name: 'MERGED LIB: deepTools'
+        anchor: 'mlib_deeptools'
         info: 'This section of the report shows QC plots generated by deepTools.'
+    - featureCounts:
+        name: 'MERGED LIB: featureCounts'
+        anchor: 'mlib_featurecounts'
+        info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
         path_filters:
-            - '*.plot*'
+            - './macs/mergedLibrary/consensus/*.summary'
     - samtools:
-        name: 'SAMTools (merged replicate; filtered)'
-        info: 'This section of the report shows SAMTools results after merging replicates and before filtering.'
+        name: 'MERGED REP: SAMTools'
+        info: 'This section of the report shows SAMTools results after merging replicates and filtering.'
         path_filters:
-            - '*mRp.clN*'
+            - './alignment/mergedReplicate/*'
     - picard:
-        name: 'Picard (merged replicate; filtered)'
+        name: 'MERGED REP: Picard'
+        anchor: 'mrep_picard'
         info: 'This section of the report shows picard results after merging libraries and before filtering.'
         path_filters:
-            - '*mRp.clN*'
+            - './alignment/mergedReplicate/*'
     - featureCounts:
-        name: 'featureCounts (merged library)'
-        info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
-        path_filters:
-            - '*mLb.clN.featureCounts*'
-    - featureCounts:
-        name: 'featureCounts (merged replicate)'
+        name: 'MERGED REP: featureCounts'
+        anchor: 'mrep_featurecounts'
         info: 'This section of the report shows featureCounts results for the number of reads assigned to merged replicate consensus peaks.'
         path_filters:
-            - '*mRp.clN.featureCounts*'
+            - './macs/mergedReplicate/consensus/*.summary'
 
 report_section_order:
     mlib_peak_count:
-        order: -1000
-    mrep_peak_count:
-        order: -1100
+        before: mlib_deeptools
     mlib_frip_score:
-        order: -1200
-    mrep_frip_score:
-        order: -1300
+        before: mlib_peak_count
     mlib_peak_annotation:
-        order: -1400
-    mrep_peak_annotation:
-        order: -1500
+        before: mlib_frip_score
+    mlib_featurecounts:
+        before: mlib_peak_annotation
     mlib_deseq2_pca:
-        order: -1600
-    mrep_deseq2_pca:
-        order: -1700
+        before: mlib_featurecounts
     mlib_deseq2_clustering:
-        order: -1800
+        before: mlib_deseq2_pca
+    mrep_peak_count:
+        before: mrep_picard
+    mrep_frip_score:
+        before: mrep_peak_count
+    mrep_peak_annotation:
+        before: mrep_frip_score
+    mrep_featurecounts:
+        before: mrep_peak_annotation
+    mrep_deseq2_pca:
+        before: mrep_featurecounts
     mrep_deseq2_clustering:
-        order: -1900
+        before: mrep_deseq2_pca
     software_versions:
-        order: -2000
+        order: -1001
     nf-core-atacseq-summary:
-        order: -2100
+        order: -1002
 
 custom_plot_config:
     picard_insert_size:
@@ -135,3 +133,18 @@ extra_fn_clean_exts:
     - 'mLb'
     - 'mRp'
     - '_peaks'
+
+# # Customise the module search patterns to speed up execution time
+# #  - Skip module sub-tools that we are not interested in
+# #  - Replace file-content searching with filename pattern searching
+# #  - Don't add anything that is the same as the MultiQC default
+# # See https://multiqc.info/docs/#optimise-file-search-patterns for details
+sp:
+    cutadapt:
+        fn: '*trimming_report.txt'
+    preseq:
+        fn: '*.ccurve.txt'
+    deeptools/plotFingerprintOutRawCounts:
+        fn: '*plotFingerprint*'
+    deeptools/plotProfile:
+        fn: '*plotProfile*'