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remove all the nf-test logic from the refactor branch #198

Merged
merged 12 commits into from
Sep 21, 2023
Merged

remove all the nf-test logic from the refactor branch #198

merged 12 commits into from
Sep 21, 2023

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maxulysse
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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/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).

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github-actions bot commented Sep 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0f9e5ea

+| ✅ 145 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • 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
  • 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
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-21 15:01:01

@adamrtalbot
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Could you rename the PR to say what it's doing? It's not clear from the code.

@maxulysse maxulysse changed the title Only refactor remove all the nf-test logic from the refactor branch Sep 21, 2023
@maxulysse maxulysse merged commit a815cf1 into nf-core:refactor Sep 21, 2023
10 checks passed
@maxulysse maxulysse deleted the only_refactor branch September 21, 2023 15:21
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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@maxulysse @adamrtalbot @nf-core-bot