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Config changes for release 2.0.0 - #88

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nikhil wants to merge 2 commits into
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Config changes for release 2.0.0#88
nikhil wants to merge 2 commits into
devfrom
feature/release_2.0.0

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@nikhil

@nikhil nikhil commented Apr 23, 2026

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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 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).

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github-actions Bot commented Apr 23, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 560f910

+| ✅ 184 tests passed       |+
#| ❔  15 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-neoantigenpipeline_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-neoantigenpipeline_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-neoantigenpipeline_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
  • nextflow_config - nextflow_config
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-neoantigenpipeline_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-neoantigenpipeline_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-neoantigenpipeline_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/neoantigen-pipeline/neoantigen-pipeline/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-21 15:34:25

Base automatically changed from feature/release_1.4.0 to dev May 8, 2026 21:05
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@nikhil