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Add --seed #395

Merged
merged 3 commits into from
Mar 8, 2022
Merged

Add --seed #395

merged 3 commits into from
Mar 8, 2022

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d4straub
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@d4straub d4straub commented Mar 8, 2022 •
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Adds --seed with default 100.

The way I implemented it now has a drawback: when re-running the pipeline with a different --seed and -resume, the processes will not re-run (i.e. uses cached processes) and use the previous seed. Because of that, I also added the seed into the log files of the runs. The implementation follows nf-core best practice, but I can also divert and implement it in a way that it will re-run processes when resuming with a different seed.

Closes #386

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/ampliseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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 Mar 8, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f0a368c

+| ✅ 138 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-03-08 14:56:56

@d4straub d4straub mentioned this pull request Mar 8, 2022
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erikrikarddaniel
erikrikarddaniel approved these changes Mar 8, 2022
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LGTM.

@d4straub d4straub merged commit beee127 into nf-core:dev Mar 8, 2022
@d4straub d4straub deleted the add-seed branch March 8, 2022 15:20
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@d4straub @erikrikarddaniel