fix: make sniffing more robust by reading full lines

fix #1561

nf_core/pipeline-template/bin/check_samplesheet.py

@@ -129,6 +129,16 @@ def validate_unique_samples(self):
                     row[self._sample_col] = f"{sample}_T{seen[sample]}"
 
 
+def read_head(handle, num_lines=10):
+    """Read the specified number of lines from the current position in the file."""
+    lines = []
+    for idx, line in enumerate(handle):
+        if idx == num_lines:
+            break
+        lines.append(line)
+    return "".join(lines)
+
+
 def sniff_format(handle):
     """
     Detect the tabular format.
@@ -144,13 +154,13 @@ def sniff_format(handle):
         https://docs.python.org/3/glossary.html#term-text-file
 
     """
-    peek = handle.read(2048)
+    peek = read_head(handle)
+    handle.seek(0)
     sniffer = csv.Sniffer()
     if not sniffer.has_header(peek):
         logger.critical(f"The given sample sheet does not appear to contain a header.")
         sys.exit(1)
     dialect = sniffer.sniff(peek)
-    handle.seek(0)
     return dialect