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Final pre-release 1.1.0 updates #175

Merged
merged 7 commits into from
Feb 23, 2024
Merged

Final pre-release 1.1.0 updates #175

merged 7 commits into from
Feb 23, 2024

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subwaystation
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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
  • If necessary, also make a PR on the nf-core/pangenome branch on the nf-core/test-datasets repository.
  • 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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github-actions bot commented Feb 23, 2024 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit d4168fb

+| ✅ 179 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   8 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowPangenome.groovy
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in WorkflowPangenome.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: wfmash_hg_filter_ani_diff

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-pangenome_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-23 13:03:15

@subwaystation subwaystation merged commit ac2ebd7 into dev Feb 23, 2024
14 of 15 checks passed
@subwaystation subwaystation deleted the final_prerelease_1.1.0_updates branch February 26, 2024 15:10
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