Kaiju: fix "division by zero"

.github/workflows/changelog.py

@@ -374,7 +374,7 @@ def _skip_existing_entry_for_this_pr(line, same_section=True):
                 updated_lines.append("\n")
                 _updated_lines = [_l for _l in section_lines + new_lines if _l.strip()]
                 if section == "### Module updates":
-                    _updated_lines = sorted(_updated_lines)
+                    _updated_lines = sorted(_updated_lines, key=lambda x: x.lower())
                 updated_lines.extend(_updated_lines)
                 updated_lines.append("\n")
                 if new_lines:

CHANGELOG.md

@@ -29,10 +29,11 @@ Highlights:
 
 ### Module updates
 
-- **Pangolin**: update for v4: add QC Note , update tool versions columns ([#2157](https://github.com/ewels/MultiQC/pull/2157))
 - **fastp**: add version parsing ([#2159](https://github.com/ewels/MultiQC/pull/2159))
 - **fastp**: correctly parse sample name from --in1/--in2 command. Prefer file name if not `fastp.json`; fallback to file name when error ([#2139](https://github.com/ewels/MultiQC/pull/2139))
+- **Kaiju**: fix "division by zero" ([#2179](https://github.com/ewels/MultiQC/pull/2179))
 - **Nanostat**: account for both tab and spaces in v1.41+ search pattern ([#2155](https://github.com/ewels/MultiQC/pull/2155))
+- **Pangolin**: update for v4: add QC Note , update tool versions columns ([#2157](https://github.com/ewels/MultiQC/pull/2157))
 - **Picard**: Generalize to directly support Sentieon and Parabricks outputs ([#2110](https://github.com/ewels/MultiQC/pull/2110))
 - **Sentieon**: Removed the module in favour of directly supporting parsing by the **Picard** module. Note that any code that relies on the module name needs to be updated, e.g. `-m sentieon` will no longer work, the exported plot and data files will be prefixed as `picard` instead of `sentieon`, etc. Note that the Sentieon module used to fetch the sample names from the file names by default, and now it follows the Picard module's logic, and prioritizes the commands recorded in the logs. To override, use the `use_filename_as_sample_name` config flag ([#2110](https://github.com/ewels/MultiQC/pull/2110))
 

multiqc/modules/kaiju/kaiju.py

@@ -170,23 +170,22 @@ def kaiju_stats_table(self):
         }
         tdata = {}
         for s_name, d in self.kaiju_sample_total_readcounts.items():
-            tdata[s_name] = {}
-            tdata[s_name]["% Unclassified"] = (
-                self.kaiju_sample_unclassified[s_name] * 100 / self.kaiju_sample_total_readcounts[s_name]
-            )
+            tdata[s_name] = {
+                # Default values in case if data is not available for this sample at this rank
+                "assigned": 0,
+                "% Assigned": 0,
+            }
+            total = self.kaiju_sample_total_readcounts[s_name]
+            if total == 0:
+                continue
+            tdata[s_name]["% Unclassified"] = self.kaiju_sample_unclassified[s_name] * 100 / total
             if s_name in self.kaiju_data[general_taxo_rank.lower()]:
                 tdata[s_name]["assigned"] = (
-                    self.kaiju_sample_total_readcounts[s_name]
+                    total
                     - self.kaiju_sample_unclassified[s_name]
                     - self.kaiju_data[general_taxo_rank.lower()][s_name]["cannot be assigned"]["count"]
                 )
-                tdata[s_name]["% Assigned"] = (
-                    tdata[s_name]["assigned"] * 100 / self.kaiju_sample_total_readcounts[s_name]
-                )
-            else:
-                # don't have the value for this samples at this rank
-                tdata[s_name]["assigned"] = 0
-                tdata[s_name]["% Assigned"] = 0
+                tdata[s_name]["% Assigned"] = tdata[s_name]["assigned"] * 100 / total
         self.general_stats_addcols(tdata, headers)
 
     def top_five_barplot(self):