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Release 2.3 - This time for real #244

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merged 6 commits into from
Jun 17, 2024
Merged

Release 2.3 - This time for real #244

merged 6 commits into from
Jun 17, 2024

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WackerO
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@WackerO WackerO commented Jun 17, 2024 •
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Second release PR after I found a bug in the previous one

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
  • 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).

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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 @WackerO,

It looks like this pull-request is has been made against the qbic-pipelines/rnadeseq 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 qbic-pipelines/rnadeseq 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 Jun 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 169e70e

+| ✅ 171 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3
  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-17 12:27:46

skrakau
skrakau reviewed Jun 17, 2024
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CHANGELOG.md Outdated Show resolved Hide resolved
@WackerO @skrakau
Update CHANGELOG.md
169e70e 
Co-authored-by: Sabrina Krakau <[email protected]>
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skrakau commented Jun 17, 2024

Even if the PR does not contain a lot of changes, it would be helpful (and best-practice) to briefly describe what this PR is about, and what the previous bug was about.

LaurenceKuhl
LaurenceKuhl reviewed Jun 17, 2024
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nextflow_schema.json
@@ -193,6 +193,16 @@
"type": "string",
"default": "${projectDir}/assets/references.bibtex",
"description": "Reference bibtex file for the report, should not be changed."
},
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why is it a variable if it shouldn't be changed?

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There was apparently some nextflow change; now it seems the files in assets/ cannot be accessed by processes unless they are provided to the respective module as channels.

skrakau
skrakau approved these changes Jun 17, 2024
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Apart from the typo it looks good to me!

@WackerO WackerO merged commit 163c7ee into master Jun 17, 2024
35 of 36 checks passed
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@LaurenceKuhl LaurenceKuhl LaurenceKuhl approved these changes

@skrakau skrakau skrakau approved these changes

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3 participants
@WackerO @skrakau @LaurenceKuhl