From 6a20d9f09e41fb3fc3290997c2b940e8b3fe3615 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 16 May 2022 11:44:19 +0200
Subject: [PATCH] fix: make sniffing more robust by reading full lines

fix #1561
---
 nf_core/pipeline-template/bin/check_samplesheet.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/bin/check_samplesheet.py b/nf_core/pipeline-template/bin/check_samplesheet.py
index d1a9919eec..3652c63c8b 100755
--- a/nf_core/pipeline-template/bin/check_samplesheet.py
+++ b/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