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Template update to 3.0.2 #16

Merged
merged 19 commits into from
Nov 19, 2024
Merged

Template update to 3.0.2 #16

merged 19 commits into from
Nov 19, 2024

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famosab
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@famosab famosab commented Nov 19, 2024 •
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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
  • 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 Nov 19, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1979686

+| ✅ 159 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config variable not found: validation.help.beforeText
  • nextflow_config - Config variable not found: validation.help.afterText
  • nextflow_config - Config variable not found: validation.summary.beforeText
  • nextflow_config - Config variable not found: validation.summary.afterText
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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!
  • schema_description - Ungrouped param in schema: dict

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-vcftomaf_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-vcftomaf_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-vcftomaf_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/test_full.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • 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/PULL_REQUEST_TEMPLATE.md
  • 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 ignored due to lint config: assets/nf-core-vcftomaf_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-vcftomaf_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-vcftomaf_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/vcftomaf/vcftomaf/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-19 14:44:09

@famosab famosab mentioned this pull request Nov 19, 2024
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d4straub
d4straub approved these changes Nov 19, 2024
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Looks good to me!

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FriederikeHanssen
FriederikeHanssen approved these changes Nov 19, 2024
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Looks good. Any chance we can get the subway map in for the 1.1. release as well?

FriederikeHanssen
FriederikeHanssen reviewed Nov 19, 2024
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famosab commented Nov 19, 2024

Looks good. Any chance we can get the subway map in for the 1.1. release as well?

its on my list I just wanted to do the template first and then subway map, handling of the error with freebayes and updated modules :)

famosab and others added 2 commits November 19, 2024 15:42
@famosab @FriederikeHanssen
Update nextflow.config
62f97a9 
Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
@famosab @FriederikeHanssen
Update assets/multiqc_config.yml
1979686 
Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
@famosab famosab merged commit f6f98a8 into qbic-pipelines:dev Nov 19, 2024
4 checks passed
@famosab famosab deleted the template-update branch November 19, 2024 14:55
@famosab famosab mentioned this pull request Nov 19, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@d4straub d4straub d4straub approved these changes

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@famosab @FriederikeHanssen @d4straub