Mosdepth: Add additional summaries to general stats

CHANGELOG.md

@@ -15,6 +15,8 @@
 
 ### Module updates
 
+- **mosdepth**: Add additional summaries to general stats #2257 ([#2257](https://github.com/MultiQC/MultiQC/pull/2257))
+
 ## [MultiQC v1.19](https://github.com/ewels/MultiQC/releases/tag/v1.19) - 2023-12-18
 
 ### MultiQC updates

docs/modules/mosdepth.md

@@ -90,8 +90,7 @@ This will then print a debug log message (use `multiqc -v`) for each excluded co
 This is disabled by default as there can be very many in some cases.
 
 Besides the `{prefix}.mosdepth.global.dist.txt` and `{prefix}.mosdepth.region.dist.txt`
-files, the `{prefix}.mosdepth.summary.txt` file is used to get the mean coverage for the
-General Stats table.
+files, the `{prefix}.mosdepth.summary.txt` file is used for the General Stats table.
 
 The module also plots an X/Y relative chromosome coverage per sample. By default, it finds chromosome named X/Y or chrX/chrY, but that can be customised:
 

multiqc/modules/mosdepth/mosdepth.py

@@ -134,7 +134,11 @@ def __init__(self):
                 # assume it will override the information collected for "total":
                 if line.startswith("total\t") or line.startswith("total_region\t"):
                     contig, length, bases, mean, min_cov, max_cov = line.split("\t")
-                    genstats[s_name]["mean_coverage"] = mean
+                    genstats[s_name]["mean_coverage"] = float(mean)
+                    genstats[s_name]["min_coverage"] = float(min_cov)
+                    genstats[s_name]["max_coverage"] = float(max_cov)
+                    genstats[s_name]["coverage_bases"] = int(bases)
+                    genstats[s_name]["length"] = int(length)
                     self.add_data_source(f, s_name=s_name, section="summary")
 
         # Filter out any samples from --ignore-samples
@@ -320,13 +324,44 @@ def __init__(self):
                 self.genstats_cov_thresholds(genstats, genstats_headers, cumcov_dist_data, threshs, hidden_threshs)
                 self.genstats_mediancov(genstats, genstats_headers, cumcov_dist_data)
 
-        # Add mean coverage to General Stats
-        genstats_headers["mean_coverage"] = {
-            "title": "Mean Cov.",
-            "description": "Mean coverage",
-            "min": 0,
-            "suffix": "X",
-            "scale": "BuPu",
+        # Add mosdepth summary to General Stats
+        genstats_headers = {
+            "mean_coverage": {
+                "title": "Mean Cov.",
+                "description": "Mean coverage",
+                "min": 0,
+                "scale": "BuPu",
+            },
+            "min_coverage": {
+                "title": "Min Cov.",
+                "description": "Minimum coverage",
+                "min": 0,
+                "scale": "BuPu",
+                "hidden": True,
+            },
+            "max_coverage": {
+                "title": "Max Cov.",
+                "description": "Maximum coverage",
+                "min": 0,
+                "scale": "BuPu",
+                "hidden": True,
+            },
+            "coverage_bases": {
+                "title": f"{config.base_count_prefix} Total Coverage Bases",
+                "description": f"Total coverage of bases ({config.base_count_desc})",
+                "min": 0,
+                "shared_key": "base_count",
+                "scale": "Greens",
+                "hidden": True,
+            },
+            "length": {
+                "title": "Genome length",
+                "description": "Total length of the genome",
+                "min": 0,
+                "scale": "Greys",
+                "format": "{:,d}",
+                "hidden": True,
+            },
         }
         self.general_stats_addcols(genstats, genstats_headers)