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fix(nextflow-development): quote samplesheet fields with csv.writer #1305

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fix(nextflow-development): quote samplesheet fields with csv.writer #1305

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13 changes: 7 additions & 6 deletions bio-research/skills/nextflow-development/scripts/generate_samplesheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
"""

import argparse
import csv
import os
import sys
from pathlib import Path
Expand Down Expand Up @@ -327,11 +328,13 @@ def _write_samplesheet(rows: List[Dict], config: Dict, output_path: str):
# Maintain original column order
active_columns = [c for c in column_names if c in active_columns]

with open(output_path, 'w') as f:
f.write(','.join(active_columns) + '\n')
# csv.writer quotes values containing commas or quotes (e.g. a path
# like "reads,run/x.fastq.gz"), which a plain ','.join would split.
with open(output_path, 'w', newline='') as f:
writer = csv.writer(f, lineterminator='\n')
writer.writerow(active_columns)
for row in rows:
values = [str(row.get(col, '')) for col in active_columns]
f.write(','.join(values) + '\n')
writer.writerow([str(row.get(col, '')) for col in active_columns])


def _print_preview(rows: List[Dict], config: Dict):
Expand All @@ -351,8 +354,6 @@ def _print_preview(rows: List[Dict], config: Dict):

def validate_existing_samplesheet(csv_path: str, pipeline: str) -> ValidationResult:
"""Validate an existing samplesheet file."""
import csv

if not os.path.exists(csv_path):
return ValidationResult(valid=False, errors=[f"File not found: {csv_path}"])

Expand Down
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