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fix(nextflow-development): quote samplesheet fields with csv.writer - #1305
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_write_samplesheet joined values with ','.join, so a FASTQ/BAM path containing a comma (e.g. "reads,run/sample_R1_001.fastq.gz") was split across several columns. The script reported success, but the file had more data fields than header fields and failed its own --validate. Write rows with csv.writer instead, keeping '\n' line endings so output for ordinary paths is unchanged. Fixes anthropics#1296
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Summary
_write_samplesheetingenerate_samplesheet.pybuilt rows with','.join, so a FASTQ/BAM path containing a comma (e.g.reads,run/sample_R1_001.fastq.gz) was split across several columns. The script reported success, but the resulting file had more data fields than header fields and failed the script's own--validatecheck.Changes
csv.writer, which quotes fields containing commas or quotes.\nline endings (lineterminator='\n',newline=''), so output for ordinary paths is byte-for-byte unchanged.import csvto module level (it was previously imported locally invalidate_existing_samplesheet).Fixes #1296