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note on '--tools' in Quickstart#1166

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maxulysse merged 5 commits intonf-core:devfrom
ATpoint:master
Aug 15, 2023
Merged

note on '--tools' in Quickstart#1166
maxulysse merged 5 commits intonf-core:devfrom
ATpoint:master

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@ATpoint
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@ATpoint ATpoint commented Jul 28, 2023 •
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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/sarek 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).

@ATpoint ATpoint requested a review from maxulysse as a code owner July 28, 2023 08:30
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github-actions bot commented Jul 28, 2023

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 @ATpoint,

It looks like this pull-request is has been made against the ATpoint/sarek 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 ATpoint/sarek 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!

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ATpoint commented Jul 28, 2023

Mention --tools in Quickstart, responding to https://www.biostars.org/p/9570657/

@ATpoint ATpoint changed the base branch from master to dev July 28, 2023 08:32
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github-actions bot commented Jul 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ba4cf5

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-15 13:33:19

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asp8200 commented Jul 28, 2023

@nf-core-bot fix linting please

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asp8200 commented Jul 28, 2023

@ATpoint : Thanks for the PR. I'm afraid you should have made the PR from ATpoint:dev. Can you fix that?

@FriederikeHanssen
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FriederikeHanssen commented Jul 28, 2023

Can you update the change log?

@maxulysse maxulysse merged commit 57a8026 into nf-core:dev Aug 15, 2023
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@ATpoint @asp8200 @FriederikeHanssen @maxulysse @nf-core-bot