Fix issues and improvements from first release

assets/multiqc_config.yaml

@@ -15,6 +15,24 @@ show_analysis_time: False
 ## Number formatting
 thousandsSep_format: " "
 
+## General Statistics table
+table_columns_visible:
+  Duplicats: False
+  ContaminationSearch - RNA: True
+  samtools: False
+  ReadsStats:
+    percent_duplicates: False
+    percent_fails: False
+  AlignmentStat:
+    avg_gc: False
+    1_x_pc: True
+    5_x_pc: True
+    10_x_pc: True
+    50_x_pc: False
+    mapped_reads: False
+    total_reads: True
+    general_error_rate: True
+
 ## Sample name formatting
 extra_fn_clean_exts:
   - "_filtered"
@@ -33,18 +51,13 @@ report_section_order:
         order: -1000
     summary:
         order: -1001
-        
+
 module_order:
   - fastqc:
         name: "ReadsStats"
         #info: "Analysis performed with FastQC, which is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge"
         href: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
         target: "FastQC"
-  - qualimap:
-        name: "AlignmentStat"
-        #info: "Analysis performed with QualiMap"
-        href: "http://qualimap.bioinfo.cipf.es/"
-        target: "QualiMap"
   - samtools:
   - fastp:
         name: "Duplicats"
@@ -54,6 +67,19 @@ module_order:
         name: "ContaminationSearch"
         #info: "This section shows the module with different files"
         target: "FastQ-Screen"
+  - sortmerna:
+        name: "ContaminationSearch - rRNA"
+        target: "SortMeRNA"
+  - qualimap:
+        name: "AlignmentStat"
+        #info: "Analysis performed with QualiMap"
+        href: "http://qualimap.bioinfo.cipf.es/"
+        target: "QualiMap"
+  - salmon:
+        name: "AlignmentStat"
+        href: "https://combine-lab.github.io/salmon/"
+        target: "Salmon"
+
 
 # Pattern
 sp: