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Document DuckDB temporary storage environment variables. - #238

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johandahlberg merged 5 commits into
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add-info-on-tmp-dir-env-vars
Aug 4, 2026
Merged

Document DuckDB temporary storage environment variables.#238
johandahlberg merged 5 commits into
devfrom
add-info-on-tmp-dir-env-vars

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@johandahlberg

@johandahlberg johandahlberg commented Aug 3, 2026 •
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Document how to configure DuckDB temporary storage environment variables.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pixelator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@johandahlberg @cursoragent
Document DuckDB temporary storage environment variables.
6f5f693 
Co-authored-by: Cursor <cursoragent@cursor.com>
@johandahlberg
johandahlberg requested a review from Aratz August 3, 2026 14:46
@johandahlberg
johandahlberg requested a review from a team as a code owner August 3, 2026 14:46
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github-actions Bot commented Aug 3, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

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github-actions Bot commented Aug 3, 2026 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 1d7ba64

+| ✅ 234 tests passed       |+
#| ❔   9 tests were ignored |#
Details

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: tests/default.nf.test
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-04 14:02:19

Aratz
Aratz approved these changes Aug 4, 2026
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Comment thread docs/usage.md Outdated
johandahlberg and others added 3 commits August 4, 2026 08:10
@johandahlberg
johandahlberg merged commit fb54d3d into dev Aug 4, 2026
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@Aratz Aratz Aratz approved these changes

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@johandahlberg @Aratz