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added nanolyse to subworkflow for qc #258

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added nanolyse to subworkflow for qc #258

wants to merge 1 commit into from

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RareSeas-Asimov
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PR checklist

  • [ X] Added Nanolyse to qc
  • 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/nanoseq 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).

@github-actions GitHub Actions
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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 @RareSeas-Asimov,

It looks like this pull-request is has been made against the RareSeas-Asimov/nanoseq 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 RareSeas-Asimov/nanoseq 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!

@RareSeas-Asimov RareSeas-Asimov changed the base branch from master to dev November 29, 2023 17:55
@github-actions GitHub Actions
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github-actions bot commented Nov 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 83f4192

+| ✅ 156 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.1.0'
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-11-29 20:25:06

@yuukiiwa
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yuukiiwa commented Nov 29, 2023 •
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Hi Adelaide (tagging you here @RareSeas-Asimov),

Thanks for the PR! But I don't think this is where your PR should be merged because this changes the nf-core/modules incorporated, which will make the pipeline not pass nf-core linting.

You should instead create three PRs in nf-core/modules: two to update the versions of the nanolyse and nanoplot modules and one to add a subworkflow for both nanolyse and nanoplot.

Thanks!

Best wishes,
Yuk Kei

@yuukiiwa yuukiiwa closed this Jul 13, 2024
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@RareSeas-Asimov @yuukiiwa