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fix: compare samplesheet enum values as strings in validator #396

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fix: compare samplesheet enum values as strings in validator #396

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5 changes: 4 additions & 1 deletion bio-research/skills/nextflow-development/scripts/utils/validators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,10 @@ def validate_samplesheet(
if col_name in row and row[col_name] and "allowed" in col_config:
value = row[col_name]
allowed = col_config["allowed"]
if value not in allowed:
# Samplesheet values are read from CSV as strings (e.g. "0"),
# while enum lists may be typed (e.g. integers [0, 1]).
# Compare as strings so typed enums still validate correctly.
if str(value) not in [str(a) for a in allowed]:
errors.append(
f"Row {row_num}: Invalid value '{value}' for '{col_name}'. "
f"Allowed: {allowed}"
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