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be compliant with black defaults
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fabianegli committed Aug 31, 2022
1 parent f105f49 commit 7faef57
Showing 1 changed file with 5 additions and 2 deletions.
7 changes: 5 additions & 2 deletions nf_core/pipeline-template/bin/check_samplesheet.py
Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,9 @@ def _validate_pair(self, row):
"""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
Expand Down Expand Up @@ -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()
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