Support flat config and table_id as a group. Add docs

docs/core/reports/customisation.md

@@ -760,6 +760,27 @@ table_columns_visible:
 Note that you can set these values to `True` to show columns that would otherwise be hidden
 by default.
 
+It can also be done for other module-specific tables in the report, where instead of
+the _Group_, you'd need to specify the table ID. To get the table ID, click
+_Configure Columns_ above the table, and look for the first line above the table contents.
+It should say something like "Uncheck the tick box ... Table ID: `quast_table`".
+
+For example, to hide the _# misassemblies_ column in the _Assembly Statistics_ table
+from QUAST, you would use the following config:
+
+```yaml
+table_columns_visible:
+  quast_table:
+    "# misassemblies": false
+```
+
+Or you can pass the column ID directly:
+
+```yaml
+table_columns_visible:
+  "# misassemblies": false
+```
+
 ### Column order
 
 In the same way, you can force a column to appear at the start or end of the table, or
@@ -796,6 +817,9 @@ table_columns_name:
     percent_gc: "Percent of bases that are GC"
 ```
 
+It will also work for module-specific tables by using the table ID instead of the module name, and specifying the column ID directly.
+See the [Hiding columns](#hiding-columns) section above for more details.
+
 ### Conditional formatting
 
 It's possible to highlight values in tables based on their value. This is done using the `table_cond_formatting_rules` config setting.

multiqc/modules/quast/quast.py

@@ -254,6 +254,7 @@ def quast_table(self):
         config = {
             "id": "quast_table",
             "min": 0,
+            "namespace": "QUAST",
         }
         return table.plot(self.quast_data, headers, config)
 

multiqc/plots/table_object.py

@@ -156,33 +156,41 @@ def __init__(self, data, headers=None, pconfig=None):
                     for cpc_k, cpc_v in config.custom_plot_config[pconfig["id"]].items():
                         headers[idx][k][cpc_k] = cpc_v
 
-                # Overwrite hidden if set in user config
-                for ns in config.table_columns_visible.keys():
-                    # Make namespace key case-insensitive
-                    if ns.lower() == headers[idx][k]["namespace"].lower():
+                # Overwrite "hidden" if set in user config
+                # Key can be a column ID, a table ID, or a namespace in the general stats table.
+                for key in config.table_columns_visible.keys():
+                    # Case-insensitive check if the outer key is a table ID or a namespace.
+                    if key.lower() == pconfig["id"].lower() or key.lower() == headers[idx][k]["namespace"].lower():
                         # First - if config value is a bool, set all module columns to that value
-                        if isinstance(config.table_columns_visible[ns], bool):
-                            headers[idx][k]["hidden"] = not config.table_columns_visible[ns]
-
-                        # Not a bool, assume a dict of the specific column IDs
-                        else:
-                            try:
-                                # Config has True = visibile, False = Hidden. Here we're setting "hidden" which is inverse
-                                headers[idx][k]["hidden"] = not config.table_columns_visible[ns][k]
-                            except KeyError:
-                                pass
-
-                # Overwrite name if set in user config
-                for ns in config.table_columns_name.keys():
-                    # Make namespace key case insensitive
-                    if ns.lower() == headers[idx][k]["namespace"].lower():
-                        # Assume a dict of the specific column IDs
-                        try:
-                            headers[idx][k]["title"] = config.table_columns_name[ns][k]
-                        except KeyError:
-                            pass
-
-                # Also overwite placement if set in config
+                        if isinstance(config.table_columns_visible[key], bool):
+                            # Config has True = visible, False = Hidden. Here we're setting "hidden" which is inverse
+                            headers[idx][k]["hidden"] = not config.table_columns_visible[key]
+
+                        # Not a bool, assume a dict of specific column IDs
+                        elif k in config.table_columns_visible[key]:
+                            # Config has True = visible, False = Hidden. Here we're setting "hidden" which is inverse
+                            headers[idx][k]["hidden"] = not config.table_columns_visible[key][k]
+
+                    # Case-insensitive check if the outer key is a column ID
+                    elif key.lower() == k.lower():
+                        if isinstance(config.table_columns_visible[key], bool):
+                            # Config has True = visible, False = Hidden. Here we're setting "hidden" which is inverse
+                            headers[idx][k]["hidden"] = not config.table_columns_visible[key]
+
+                # Overwrite "name" if set in user config
+                # Key can be a column ID, a table ID, or a namespace in the general stats table.
+                for key in config.table_columns_name.keys():
+                    # Case-insensitive check if the outer key is a table ID or a namespace.
+                    if key.lower() == pconfig["id"].lower() or key.lower() == headers[idx][k]["namespace"].lower():
+                        # Assume a dict of specific column IDs
+                        headers[idx][k]["title"] = config.table_columns_name[key][k]
+
+                    # Case-insensitive check if the outer key is a column ID
+                    elif key.lower() == k.lower():
+                        if isinstance(config.table_columns_visible[key], bool):
+                            headers[idx][k]["title"] = config.table_columns_visible[key]
+
+                # Also overwrite placement if set in config
                 try:
                     headers[idx][k]["placement"] = float(
                         config.table_columns_placement[headers[idx][k]["namespace"]][k]