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Parabricks alignment #1444

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wants to merge 8 commits into from
Closed

Parabricks alignment #1444

wants to merge 8 commits into from

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Furentsu
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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).

@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 @Furentsu,

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

@github-actions GitHub Actions
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github-actions bot commented Mar 20, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3c05085

+| ✅ 181 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-11 13:43:56

@Furentsu Furentsu self-assigned this Mar 21, 2024
@Furentsu Furentsu added the help wanted Extra attention is needed label Mar 21, 2024
@maxulysse maxulysse changed the base branch from master to dev March 27, 2024 13:52
maxulysse
maxulysse reviewed Apr 4, 2024
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@maxulysse maxulysse left a comment

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So looking fairly good, I have some ideas for improvements.
Sorry it took so long to check it out properly.
I'll be merging #1422 soon.
Do you mind if I push some commits here afterwards to ease the pain of solving the merge conflicts?

@Furentsu
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Furentsu commented Apr 4, 2024

No problem, thanks for helping out :)

@Furentsu
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Furentsu commented Apr 9, 2024

Hi @maxulysse, is there anything else I should do to merge this PR?

@maxulysse
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Hi @maxulysse, is there anything else I should do to merge this PR?

I was thinking more doing a release this week and then merging it in, as this would be a major change, and that would be a good point for introducing a bit of refactoring.

I'll try to have a look and solve all merge conflicts once we merged #1457

@maxulysse maxulysse added this to the 3.5 milestone May 7, 2024
@Furentsu Furentsu requested a review from maxulysse June 19, 2024 08:57
@FriederikeHanssen FriederikeHanssen removed this from the 3.5 milestone Aug 19, 2024
@Furentsu Furentsu closed this Oct 25, 2024
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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

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@Furentsu Furentsu

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@Furentsu @maxulysse @FriederikeHanssen