Quote CSV values only when required - #7377
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Pull request overview
This PR updates Nextflow’s CsvWriter so it only quotes CSV headers and field values when necessary to produce valid CSV (e.g., values containing separators, quotes, or CR/LF), addressing readability and downstream parsing issues (e.g., index files used with .splitCsv).
Changes:
- Emit unquoted fields by default; quote only when required and escape embedded double quotes using the doubled-quote CSV convention.
- Apply the same conditional-quoting logic to headers.
- Expand unit tests to cover separators, quotes, CR/LF, empty/null values, and custom separators.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
modules/nextflow/src/main/groovy/nextflow/util/CsvWriter.groovy |
Introduces conditional quoting/escaping via formatCsvValue and applies it to headers and row values. |
modules/nextflow/src/test/groovy/nextflow/util/CsvWriterTest.groovy |
Updates existing expectations and adds coverage for quoting/escaping behavior and custom separators. |
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bentsherman
self-requested a review
July 22, 2026 19:52
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Summary
Tests
./gradlew :nextflow:test --tests nextflow.util.CsvWriterTestCloses #5546