Default general stats column display and ordering

conf/multiqc_config.yaml

@@ -21,7 +21,77 @@ top_modules:
      - 'qualimap'
      - 'damageprofiler'
      - 'gatk'
-
+qualimap_config:
+    general_stats_coverage:
+        - 1
+        - 2
+        - 3
+        - 4
+        - 5
+table_columns_visible:
+    FastQC (pre-AdapterRemoval):
+        percent_duplicates: False
+        percent_gc: True
+        avg_sequence_length: True
+    fastp:
+        pct_duplication: False
+        after_filtering_gc_content: True
+        pct_surviving: False
+    Adapter Removal:
+        aligned_total: False
+        percent_aligned: True
+    FastQC (post-AdapterRemoval):
+        percent_duplicates: False
+        total_sequences: True
+        percent_gc: True
+    QualiMap:
+        1_x_pc: True
+        5_x_pc: True
+        percentage_aligned: False
+    DamageProfiler::
+        3 Prime1: True
+        3 Prime2: True
+        5 Prime1: True
+        5 Prime2: True
+        mean_readlength: True
+        median_readlength: True
+table_columns_placement:
+    FastQC (pre-AdapterRemoval):
+        total_sequences: 100
+        avg_sequence_length: 110
+        percent_gc: 120
+    fastp:
+        after_filtering_gc_content: 200
+    Adapter Removal:
+        percent_aligned: 300
+    FastQC (post-AdapterRemoval): 
+        total_sequences: 400
+        avg_sequence_length: 410
+        percent_gc: 420
+    Samtools Flagstat:
+        mapped_passed: 500
+    DeDup: 
+        clusterfactor: 600        
+        duplication_rate: 610
+    QualiMap:
+        median_coverage: 700
+        1_x_pc: 710
+        2_x_pc: 720
+        3_x_pc: 730
+        4_x_pc: 740
+        5_x_pc: 750
+        avg_gc: 760
+    mtnucratio:
+        mtreads: 800
+        mt_cov_avg: 810
+        mt_nuc_ratio: 820
+    DamageProfiler::
+        3 Prime1: 900
+        3 Prime2: 910
+        5 Prime1: 920
+        5 Prime2: 930
+        mean_readlength: 940
+        median_readlength: 950
 read_count_multiplier: 1
 read_count_prefix: ''
 read_count_desc: ''