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Use +profile in CI to add test to docker/conda/singularity profile #265

Merged
merged 2 commits into from
Feb 1, 2024
Merged

Use +profile in CI to add test to docker/conda/singularity profile #265

merged 2 commits into from
Feb 1, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Feb 1, 2024 •
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Changes:

  • Uses "+" syntax from nf-test to add a the test profile to pre-existing profile
  • No other changes yet, keeping the PR small
  • We can replace parts of the test config after this is implemented

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/fetchngs 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).

@adamrtalbot
Use +profile in CI to add test to docker/conda/singularity profile
80a8983 
Changes:
 - Uses "+" syntax from nf-test to add a the test profile to pre-existing profile
 - No other changes yet, keeping the PR small
 - We can replace parts of the test config after this is implemented
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github-actions bot commented Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9de329a

+| ✅ 148 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: 1.12.0
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-01 18:34:04

drpatelh
drpatelh approved these changes Feb 1, 2024
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👌🏽

@adamrtalbot adamrtalbot merged commit 8572084 into nf-core:dev Feb 1, 2024
60 checks passed
@adamrtalbot adamrtalbot deleted the make_profiles_accumulate_in_ci branch February 2, 2024 17:43
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@drpatelh drpatelh drpatelh approved these changes

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