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Fix protocol consistency #171

Merged
merged 4 commits into from
Jul 15, 2022
Merged

Fix protocol consistency #171

merged 4 commits into from
Jul 15, 2022

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apeltzer
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@apeltzer apeltzer commented Jul 14, 2022 •
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This should fix the inconsistencies between what is used in trimgalore and in mirtrace. Now keeps things the same.

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/smrnaseq 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).

@apeltzer apeltzer requested a review from a team July 14, 2022 13:05
@apeltzer apeltzer changed the base branch from master to dev July 14, 2022 13:05
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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 @apeltzer,

It looks like this pull-request is has been made against the nf-core/smrnaseq 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/smrnaseq 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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github-actions bot commented Jul 14, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5f4426b

+| ✅ 145 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-14 13:36:09

@apeltzer
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Closes #172

@apeltzer apeltzer merged commit 4286259 into dev Jul 15, 2022
@apeltzer apeltzer deleted the fix-protocol-consistency branch July 15, 2022 06:52
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