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Remove local module STARFUSION_DOWNLOAD #599

Merged
merged 3 commits into from
Dec 26, 2024
Merged

Remove local module STARFUSION_DOWNLOAD #599

merged 3 commits into from
Dec 26, 2024

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atrigila
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@atrigila atrigila commented Dec 23, 2024 •
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Closes #598

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/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • 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).

@atrigila atrigila self-assigned this Dec 23, 2024
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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: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 23, 2024 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 37a5483

+| ✅ 220 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-23 19:09:08

@atrigila atrigila marked this pull request as ready for review December 23, 2024 19:08
nschcolnicov
nschcolnicov approved these changes Dec 26, 2024
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PR looks good and makes sense.
@atrigila Do we need to update the docs/output file?
Also, I see this module was removed in the refactor references PR, do you know why we no longer need this module?

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There is no mention of this module in the docs. I think that it is no longer needed because you can either build your own starfusion reference (with STARFUSION_BUILD) or provide it ready to use as a path (for example using the plug-n-play option).

@atrigila atrigila merged commit c63fcb7 into nf-core:dev Dec 26, 2024
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@atrigila atrigila mentioned this pull request Dec 26, 2024
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@nschcolnicov nschcolnicov nschcolnicov approved these changes

@alanmmobbs93 alanmmobbs93 Awaiting requested review from alanmmobbs93

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@atrigila @nf-core-bot @nschcolnicov