From 0fb3c2636775c942dd7d21d7f02382120949dab8 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 1 Sep 2022 13:27:49 +0000
Subject: [PATCH] Template update for nf-core/tools version 2.5.1
---
bin/check_samplesheet.py | 9 ++++++---
pyproject.toml | 10 ++++++++++
2 files changed, 16 insertions(+), 3 deletions(-)
create mode 100644 pyproject.toml
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 9a8b896..11b1557 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -98,7 +98,9 @@ class RowChecker:
"""Assert that read pairs have the same file extension. Report pair status."""
if row[self._first_col] and row[self._second_col]:
row[self._single_col] = False
- if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]:
+ first_col_suffix = Path(row[self._first_col]).suffixes[-2:]
+ second_col_suffix = Path(row[self._second_col]).suffixes[-2:]
+ if first_col_suffix != second_col_suffix:
raise AssertionError("FASTQ pairs must have the same file extensions.")
else:
row[self._single_col] = True
@@ -157,7 +159,7 @@ def sniff_format(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.")
+ logger.critical("The given sample sheet does not appear to contain a header.")
sys.exit(1)
dialect = sniffer.sniff(peek)
return dialect
@@ -195,7 +197,8 @@ def check_samplesheet(file_in, file_out):
reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle))
# Validate the existence of the expected header columns.
if not required_columns.issubset(reader.fieldnames):
- logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.")
+ req_cols = ", ".join(required_columns)
+ logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.")
sys.exit(1)
# Validate each row.
checker = RowChecker()
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..0d62beb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,10 @@
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.black]
+line-length = 120
+target_version = ["py37", "py38", "py39", "py310"]
+
+[tool.isort]
+profile = "black"
+known_first_party = ["nf_core"]
+multi_line_output = 3
--
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