Attempt a rational fixed ordering of sections

Author: pinin4fjords

workflows/rnaseq/assets/multiqc/multiqc_config.yml

@@ -1,52 +1,69 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/rnaseq/tree/dev" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
+  # Important checks and failures
   sample-status:
-    order: 1104
+    order: 5004
   fail_trimmed_samples-module:
-    order: 1103
+    order: 5003
   fail_mapped_samples-module:
-    order: 1102
+    order: 5002
   fail_strand_check-module:
-    order: 1101
+    order: 5001
+  # Preprocessing and pre-alignment QC
+  fastqc_raw:
+    order: 4004
+  cutadapt:
+    order: 4003
+  fastp:
+    order: 4003
+  fastqc_trimmed:
+    order: 4002
+  # Alignment
+  star:
+    order: 3000
+  hisat2:
+    order: 3000
+  # Post-alignment QC
+  samtools:
+    order: 3000
+  dupradar-module:
+    order: 3000
   featurecounts_biotype:
-    order: 1100
+    order: 3000
+  picard:
+    order: 3000
+  preseq:
+    order: 3000
+  qualimap:
+    order: 3000
+  rseqc:
+    order: 3000
+  umitools:
+    order: 3000
+  # Quantification
+  rsem:
+    order: 2000
+  salmon:
+    order: 2000
+  kallisto:
+    order: 2000
+  # Post-quantification QC
   sample-relationships:
-    order: 1099
-  dupradar-module:
-    order: 1089
+    order: 1006
   star_salmon_deseq2_pca:
-    order: 1098
+    order: 1005
   star_salmon_deseq2_clustering:
-    order: 1087
+    order: 1004
   salmon_deseq2_pca:
-    order: 1086
+    order: 1003
   salmon_deseq2_clustering:
-    order: 1085
-  star_rsem_deseq2_pca:
-    order: 1084
-  star_rsem_deseq2_clustering:
-    order: 1083
-  picard:
-    order: 1082
-  qualimap:
-    order: 1081
-  rseqc:
-    order: 1070
-  salmon:
-    order: 1079
-  samtools:
-    order: 1078
-  star:
-    order: 1077
-  fastqc_raw:
     order: 1002
-  cutadapt:
-    order: 1001
-  fastp:
+  star_rsem_deseq2_pca:
     order: 1001
-  fastqc_trimmed:
+  star_rsem_deseq2_clustering:
     order: 1000
+  # Summaries
   "nf-core-rnaseq-methods-description-module":
     order: -1000
   "software_versions-module":