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add nf-test tests and snapshots #323

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wants to merge 14 commits into from
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add nf-test tests and snapshots #323

wants to merge 14 commits into from

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louperelo
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@louperelo louperelo commented Nov 17, 2023 •
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Closes Issue #280

The tests for test.config (AMP and ARG workflow without deparg) and test_bgc.config (BGC workflow) and test_deeparg(ARG workflow with deepARG only) have been added with their respective snapshots.
With the update of the deepARG module and the database copy on Zenodo, the deepARG-test separation might not be necessary any more.

Some questions to discuss:

  • How to test the different annotation tools (for now the tests are run with --annotation prodigal): Should there be separate tests of several tests in one file?
  • Why the test.config files are kept and not included in a setup and when block?
    To visualize what I mean here, I now added a test test_all.nf.test with snapshot. There is no corresponding test_all.config file in the conf/ folder, as all necessary parameters are added to the when{} block.
  • Do we need tests for the sub workflows only (amp.nf, bcc.nf, arg.nf)?
  • Do we need a test with snapshot for the full dataset test?
  • How do we control, which test is being triggered at which kind of activity (change on module level, sub workflow level, whole pipeline level, new version release)?

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/funcscan 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 Nov 17, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 1171c90

+| ✅ 158 tests passed       |+
!| ❗   1 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'

❗ Test warnings:

  • 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 passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-21 11:48:17

@louperelo
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@nf-core-bot fix linting

@louperelo louperelo self-assigned this Nov 21, 2023
@jfy133 jfy133 mentioned this pull request Jan 24, 2024
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@jfy133 jfy133 closed this Jan 24, 2024
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@jfy133 jfy133 Awaiting requested review from jfy133

@jasmezz jasmezz Awaiting requested review from jasmezz

@Darcy220606 Darcy220606 Awaiting requested review from Darcy220606

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