Sample Sheets >2048 character give Error: Could not determine delimiter (DSL2)

[TheodoreMarkulin]

Description of the bug

When using a particularly large sample sheet the sniff_format function is unable to determine the format of the sample sheet and returns an error. This appears to happen when the size given to handle.read is smaller than the size of the file.

Steps to reproduce

Steps to reproduce the behavior:

1. Create a large delimited samplesheet, any delimiter works so long as the samplesheet has more than 2048 characters
2. import check_samplesheet- may need to append its location into your sys.path
3. Create a pair of Path objects, one for the sample sheet, one for the file output
4. Run check_samplesheet.check_samplesheet(<IN>, <OUT>)
5. See error:

Error("Could not determine delimiter")

Additional context

Drastically upping the value given to line 147 in check_samplesheet.py fixes this issue.

methylseq/bin/check_samplesheet.py

Lines 132 to 147 in acdc4af

	def sniff_format(handle):
	"""
	Detect the tabular format.
	Args:
	handle (text file): A handle to a `text file`_ object. The read position is
	expected to be at the beginning (index 0).
	Returns:
	csv.Dialect: The detected tabular format.
	.. _text file:
	https://docs.python.org/3/glossary.html#term-text-file
	"""
	peek = handle.read(2048)

[ewels]

This was a bug in the nf-core template and should have been fixed in the latest release of nf-core/tools I believe. As such this should be resolved once #233 is merged 👍🏻

x-ref nf-core/tools#1561 and nf-core/tools#1584