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Better support for custom chemistries #273

Merged
merged 6 commits into from
Oct 30, 2023
Merged

Better support for custom chemistries #273

merged 6 commits into from
Oct 30, 2023

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grst
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@grst grst commented Oct 27, 2023 •
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Close #88
Close #189
Close #218

  • Better support for custom protocols
    • The universc protocol is now specified via the --protocol flag
    • Any protocol specified is now passed to the respective aligner
    • Added a section to the documentation

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/scrnaseq 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 --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).

@grst grst changed the title Custom chemistries Better support for custom chemistries Oct 27, 2023
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github-actions bot commented Oct 27, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit af63d84

+| ✅ 158 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-27 09:15:42

@grst grst marked this pull request as ready for review October 27, 2023 09:30
@grst grst requested a review from fmalmeida October 27, 2023 09:32
@grst grst mentioned this pull request Oct 27, 2023
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@grst grst merged commit 2a853c9 into dev Oct 30, 2023
14 checks passed
@grst grst deleted the custom-chemistries branch October 30, 2023 07:02
@grst grst mentioned this pull request Jan 2, 2024
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@fmalmeida fmalmeida fmalmeida approved these changes

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