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Fix to issue 299 and 297 #300

Merged
merged 8 commits into from
Mar 13, 2024
Merged

Fix to issue 299 and 297 #300

merged 8 commits into from
Mar 13, 2024

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heylf
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@heylf heylf commented Feb 2, 2024

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/scrnaseq 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>).
  • 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).

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github-actions bot commented Feb 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 @heylf,

It looks like this pull-request is has been made against the heylf/scrnaseq 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 heylf/scrnaseq 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!

@heylf
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heylf commented Feb 2, 2024

This PR should fix the issues 297 and 299

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github-actions bot commented Feb 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e20e897

+| ✅ 171 tests passed       |+
#| ❔   4 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-13 07:08:03

grst
grst requested changes Feb 2, 2024
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modules/local/mtx_to_seurat.nf Outdated Show resolved Hide resolved
@heylf heylf changed the base branch from master to dev February 2, 2024 14:21
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grst commented Feb 14, 2024

Now that @fmalmeida set-up nf-test, it would be great to add a testcase for cellranger-arc to make sure such issues don't arise again.

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heylf commented Feb 15, 2024

Now that @fmalmeida set-up nf-test, it would be great to add a testcase for cellranger-arc to make sure such issues don't arise again.

I agree. I assigned myself to that issue. I will do it latest before the March Hackathon.

@grst grst mentioned this pull request Mar 5, 2024
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grst commented Mar 7, 2024

@heylf, could you please take another look? I'm afraid something got screwed up by merging in the template update.

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heylf commented Mar 7, 2024

@grst yeah saw right now that this PR was still hanging nf-core/modules#4839. If its merged then it should be fine.

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grst commented Mar 11, 2024

@heylf, if you look at the diff, there's now basically no changes left since I merged in the template update.

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heylf commented Mar 11, 2024

@grst Yeah its fine to merge

@grst grst enabled auto-merge March 13, 2024 07:07
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grst approved these changes Mar 13, 2024
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LGTM

@grst grst merged commit d554870 into nf-core:dev Mar 13, 2024
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