From 8d9bae6d8dd0a78b9a40e2f6cfe40ddb16dbfa2a Mon Sep 17 00:00:00 2001 From: fabianegli Date: Tue, 30 Aug 2022 17:39:37 +0200 Subject: [PATCH 1/2] be compliant with black defaults --- nf_core/pipeline-template/bin/check_samplesheet.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/bin/check_samplesheet.py b/nf_core/pipeline-template/bin/check_samplesheet.py index 9a8b896239..6e778747c0 100755 --- a/nf_core/pipeline-template/bin/check_samplesheet.py +++ b/nf_core/pipeline-template/bin/check_samplesheet.py @@ -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 @@ -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() From 9d30b2b26423ffffd4355fbf3842faf8b59a1774 Mon Sep 17 00:00:00 2001 From: fabianegli Date: Tue, 30 Aug 2022 18:00:03 +0200 Subject: [PATCH 2/2] remove unnecessary f-string --- nf_core/pipeline-template/bin/check_samplesheet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/bin/check_samplesheet.py b/nf_core/pipeline-template/bin/check_samplesheet.py index 6e778747c0..11b155723a 100755 --- a/nf_core/pipeline-template/bin/check_samplesheet.py +++ b/nf_core/pipeline-template/bin/check_samplesheet.py @@ -159,7 +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