FastQC: Handle NaN in Sequence Content Plot

Closes #1246

CHANGELOG.md

@@ -20,6 +20,8 @@
   - Fixed bug where `QUAL` value `.` would crash MultiQC ([#1400](https://github.com/ewels/MultiQC/issues/1400))
 - **bowtie2**
   - Fix bug where HiSAT2 paired-end bar plots were missing unaligned reads ([#1230](https://github.com/ewels/MultiQC/issues/1230))
+- **FastQC**
+  - Replace `NaN` with `0` in the _Per Base Sequence Content_ plot to avoid crashing the plot ([#1246](https://github.com/ewels/MultiQC/issues/1246))
 - **Picard**
   - Fixed bug in `ValidateSamFile` module where additional whitespace at the end of the file would cause MultiQC to crash ([#1397](https://github.com/ewels/MultiQC/issues/1397))
 - **Somalier**

multiqc/modules/fastqc/fastqc.py

@@ -15,6 +15,7 @@
 import io
 import json
 import logging
+import math
 import os
 import re
 import zipfile
@@ -465,14 +466,22 @@ def sequence_content_plot(self):
                 }
             except KeyError:
                 pass
+
             # Old versions of FastQC give counts instead of percentages
             for b in data[s_name]:
                 tot = sum([data[s_name][b][base] for base in ["a", "c", "t", "g"]])
                 if tot == 100.0:
-                    break
+                    break # Stop loop after one iteration if summed to 100 (percentages)
                 else:
                     for base in ["a", "c", "t", "g"]:
                         data[s_name][b][base] = (float(data[s_name][b][base]) / float(tot)) * 100.0
+
+            # Replace NaN with 0
+            for b in data[s_name]:
+                for base in ["a", "c", "t", "g"]:
+                    if math.isnan(float(data[s_name][b][base])):
+                        data[s_name][b][base] = 0
+
         if len(data) == 0:
             log.debug("sequence_content not found in FastQC reports")
             return None