[08raviyadav]

Summary

Fixes #1296: generate_samplesheet.py reported success but wrote a malformed samplesheet whenever a FASTQ path contained a comma (for example, reads stored in a reads,run/ directory).

Cause

_write_samplesheet() assembled rows with ','.join(values), so a comma inside any value became a field separator. With a comma in the input directory, the 4-column rnaseq header was followed by a 6-field data row, and the tool's own --validate then rejected the file it had just written (missing FASTQ paths, invalid strandedness).

Change

bio-research/skills/nextflow-development/scripts/generate_samplesheet.py only:

• Write the samplesheet with csv.writer (minimal quoting, \n line terminator to keep the existing file format). Values containing commas are now quoted as single fields; values without special characters are written exactly as before.

Verification

Reproduced the issue steps locally, before and after the change:

• Before: generation exits 0, header parses as 4 fields, data row parses as 6 fields, --validate fails (exit 1).
• After: header and data row both parse as 4 fields with the comma paths quoted, and --validate passes ("Samplesheet is valid for rnaseq").
• Regression check: a comma-free input directory produces byte-identical output to the old writer.

[github-actions]

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