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Release 1.2.0 (#28) #29

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Release 1.2.0 (#28) #29

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famosab
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@famosab famosab commented Jan 15, 2025

  • bump version to 1.2.0dev

  • change version in nf-core yml

  • Template Update to 3.1.1 (Template Update to 3.1.1 #25)

  • Template update for nf-core/tools version 3.1.1

  • update Changelog

  • remove duplicate of workflow file

  • Apply suggestions from code review

  • Enable VEP annotation with vcf2maf module (Enable VEP annotation with vcf2maf module #24)

  • update vcf2maf module and vep test

  • update untar and enable vep again

  • remove .vscode

  • add test_vep to CI tests

  • final newline

  • add vep options back to usage docs

  • prepare release 1.2.0 (prepare release 1.2.0 #27)

  • prepare next release

  • prettier

  • move VEP annotation to addition

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 pipelines 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).

@famosab @mapo9
Release 1.2.0 (#28)
b59bdcb 
* bump version to 1.2.0dev

* change version in nf-core yml

* Template Update to 3.1.1 (#25)

* Template update for nf-core/tools version 3.1.1

* update Changelog

* remove duplicate of workflow file

* Apply suggestions from code review

Co-authored-by: Mark Polster <[email protected]>

---------

Co-authored-by: Mark Polster <[email protected]>

* Enable VEP annotation with vcf2maf module (#24)

* update vcf2maf module and vep test

* update untar and enable vep again

* remove .vscode

* add test_vep to CI tests

* final newline

* add vep options back to usage docs

* prepare release 1.2.0 (#27)

* prepare next release

* prettier

* move VEP annotation to addition

---------

Co-authored-by: Mark Polster <[email protected]>
@github-actions GitHub Actions
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github-actions bot commented Jan 15, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6652cfb

+| ✅ 160 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

❔ 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 3.1.1
  • Run at 2025-01-15 11:42:15

@famosab famosab closed this Jan 15, 2025
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