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417 allow skipping freyja boot #426

Merged
merged 6 commits into from
May 10, 2024
Merged

417 allow skipping freyja boot #426

merged 6 commits into from
May 10, 2024

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Joon-Klaps
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@Joon-Klaps Joon-Klaps commented May 2, 2024 •
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PR checklist

Solves issue #417, allow freyja boostrapping module to be skipped if specified by the user. + version bump of modules.

  • 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
  • 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).

@Joon-Klaps Joon-Klaps linked an issue May 2, 2024 that may be closed by this pull request
Allow skipping freyja boot #417
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github-actions bot commented May 2, 2024

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @Joon-Klaps,

It looks like this pull-request is has been made against the nf-core/viralrecon master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/viralrecon dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@Joon-Klaps Joon-Klaps changed the base branch from master to dev May 2, 2024 16:32
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github-actions bot commented May 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6160aab

+| ✅ 176 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 247]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-06 12:04:15

@Joon-Klaps
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Waiting for nf-core/modules#5555 to be merged

@Joon-Klaps Joon-Klaps marked this pull request as ready for review May 3, 2024 09:51
@Joon-Klaps Joon-Klaps requested a review from svarona May 3, 2024 09:51
@Joon-Klaps
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CI fails because of linting for a subworkflow I haven't touched 😕

@maxulysse
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CI fails because of linting for a subworkflow I haven't touched 😕

Yeah, that's a tools issue unfortunately, updating this particular subworkflow should fix the issue.
sorry about that

svarona
svarona approved these changes May 9, 2024
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ILGTM! Another issue fixed! 🥳

@Joon-Klaps Joon-Klaps merged commit c032f88 into dev May 10, 2024
24 checks passed
@Joon-Klaps Joon-Klaps deleted the 417-allow-skipping-freyja-boot branch May 10, 2024 07:37
@maxulysse
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Yeah, I feel like we're getting closer and closer to a release

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@svarona svarona svarona approved these changes

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Allow skipping freyja boot
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@Joon-Klaps @maxulysse @svarona