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Make files selected with random_preanalysis reproducible. #400

Merged
merged 7 commits into from
Aug 10, 2024
Merged

Make files selected with random_preanalysis reproducible. #400

merged 7 commits into from
Aug 10, 2024

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wfondrie
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@wfondrie wfondrie commented Aug 9, 2024 •
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This PR adds a sorting step to the input channel prior to the random selection of files. It also adds a new parameter to control the random seed.

Fixes #399.

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/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

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github-actions bot commented Aug 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a69d08f

+| ✅ 293 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-09 23:13:36

@ypriverol
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Thanks for this contribution @wfondrie !!!

@ypriverol ypriverol merged commit 70bdb1e into bigbio:dev Aug 10, 2024
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@ypriverol ypriverol ypriverol approved these changes

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Successfully merging this pull request may close these issues.

Random subset of files selected for DIANN prenalaysis is irreproducible.
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@wfondrie @ypriverol