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Try to fix CI pipeline AGAIN #1262

Merged
merged 5 commits into from
Mar 13, 2024
Merged

Try to fix CI pipeline AGAIN #1262

merged 5 commits into from
Mar 13, 2024

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adamrtalbot
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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/rnaseq 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).

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github-actions bot commented Mar 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0df628a

+| ✅ 169 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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!
  • 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

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-12 18:41:53

adamrtalbot
adamrtalbot commented Mar 12, 2024
View reviewed changes
.github/workflows/ci.yml
@@ -183,7 +182,7 @@ jobs:
test:
name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
needs: [nf-test-changes]
if: needs.nf-test-changes.outputs.changes
if: needs.nf-test-changes.outputs.tags != '[]'
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This bit was the problem, the job wasn't being skipped it was a matrix of 1.

@adamrtalbot adamrtalbot merged commit 8858f7f into nf-core:dev Mar 13, 2024
28 checks passed
@adamrtalbot adamrtalbot deleted the fix_ci_test_deps_2 branch March 13, 2024 09:24
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@maxulysse maxulysse maxulysse approved these changes

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@adamrtalbot @maxulysse