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Published 20 hours ago • verified publisher icon nf-core

Dev

Open ahepperla opened this issue 10 months ago • 3 comments

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/cutandrun 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>).
  • [ ] 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).

ahepperla avatar Apr 15 '24 19:04 ahepperla

nf-core lint overall result: Failed :x:

Posted for pipeline commit 084f5fd

+| ✅ 194 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌  10 tests failed       |-

:x: 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/WorkflowCutandrun.groovy
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • 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

:heavy_exclamation_mark: Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.2.2
  • pipeline_todos - TODO string in WorkflowCutandrun.groovy: Optionally add in-text citation tools to this list.
  • 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

:grey_question: Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-15 19:19:14

github-actions[bot] avatar Apr 15 '24 19:04 github-actions[bot]

@chris-cheshire FYI thisi s to allow loading of https://github.com/nf-core/configs/blob/master/conf/pipeline/cutandrun/unc_longleaf.config

jfy133 avatar Apr 16 '24 08:04 jfy133

@jfy133, thanks I will get this into the next release

chris-cheshire avatar Apr 26 '24 09:04 chris-cheshire