diff --git a/sunbeam/workflow/scripts/fastqc_report.py b/sunbeam/workflow/scripts/fastqc_report.py
index feeea6f6..303ac961 100755
--- a/sunbeam/workflow/scripts/fastqc_report.py
+++ b/sunbeam/workflow/scripts/fastqc_report.py
@@ -2,17 +2,22 @@
 from typing import TextIO
 
 
-def f(log: TextIO):
-    import pandas
-    from sunbeam.bfx.reports import parse_fastqc_quality
+def f(log: TextIO):
+    import pandas
+    from sunbeam.bfx.reports import parse_fastqc_quality
 
     input_reports = snakemake.input.reports  # type: ignore
     output_report = snakemake.output.report  # type: ignore
-
-    quality_list = [parse_fastqc_quality(file) for file in input_reports]
-    quality_list = [qr for qr in quality_list if qr is not None]
-    quality_table = pandas.concat(quality_list, axis=1).transpose()
-    quality_table.to_csv(output_report, sep="\t", index_label="Samples")
+
+    quality_list = [parse_fastqc_quality(file) for file in input_reports]
+    quality_list = [qr for qr in quality_list if qr is not None]
+    if len(quality_list) == 0:
+        log.write("No per-base sequence quality data found; writing empty report.\n")
+        pandas.DataFrame().to_csv(output_report, sep="\t", index_label="Samples")
+        return
+
+    quality_table = pandas.concat(quality_list, axis=1).transpose()
+    quality_table.to_csv(output_report, sep="\t", index_label="Samples")
 
 
 log_f = snakemake.log[0]  # type: ignore