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Template update for nf-core/tools version 3.0.2 #167

Merged
merged 30 commits into from
Oct 14, 2024
Merged

Template update for nf-core/tools version 3.0.2 #167

merged 30 commits into from
Oct 14, 2024

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Lucpen
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@Lucpen Lucpen commented Oct 13, 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
  • 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).

@Lucpen Lucpen requested a review from a team as a code owner October 13, 2024 11:34
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github-actions bot commented Oct 13, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8dda20d

+| ✅ 179 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 2.2.1
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-tomte_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-tomte_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-tomte_logo_dark.png
  • files_exist - File is ignored: docs/images/tomte_logo.eps
  • files_exist - File is ignored: docs/images/tomte_pipeline_metromap.eps
  • files_exist - File is ignored: docs/images/tomte_pipeline_metromap.png
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-tomte_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-tomte_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-tomte_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/tomte/tomte/.github/workflows/awstest.yml
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-14 08:56:49

@Lucpen Lucpen linked an issue Oct 13, 2024 that may be closed by this pull request
mRNA and rRNA percentages missing from MultiQC output #150
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@Lucpen Lucpen added the Ready for review Ready for review label Oct 14, 2024
fellen31
fellen31 reviewed Oct 14, 2024
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Nice!

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By the way, the MultiQC fix in the last release, is that fixed now since MultiQC is updated? If so, add MultiQC to CHANGELOG as well.

Lucpen
Lucpen commented Oct 14, 2024
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Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Lucpen
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Lucpen commented Oct 14, 2024

@fellen31 good catch with the MultiQC! I did add the issue but forgot to update CHANGELOG!

@Lucpen Lucpen requested a review from fellen31 October 14, 2024 09:16
fellen31
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Nice, then this looks good to me!

Just remembered one tiny thing in the docs.

docs/usage.md

```yaml
```yaml title="params.yaml"
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How do you see the name of params.yaml?

I think the old version is clearer.

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To be honest, I think it looks rather nice this way. It's also clear because line 324 says that it is a params file in yaml, then you see the command with it and after that how it would look, so I will leave it as it is

@Lucpen Lucpen merged commit e0046dd into dev Oct 14, 2024
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mRNA and rRNA percentages missing from MultiQC output
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@Lucpen @fellen31