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add nf-test tests and snapshots #331

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wants to merge 17 commits into from
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add nf-test tests and snapshots #331

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@jfy133 jfy133 commented Jan 24, 2024 •
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Replacing: #323

Due to some git merge issues

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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jfy133 commented Jan 24, 2024

@nf-core-bot fix linting

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github-actions bot commented Jan 24, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit ab433c1

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!
-| ❌   6 tests failed       |-

❌ Test failures:

  • 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/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/funcscan/tree/dev" target="_blank">nf-core/funcscan</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/funcscan/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/funcscan/releases/tag/dev" target="_blank">nf-core/funcscan</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/funcscan/dev/docs/output" target="_blank">documentation</a>.

❗ 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 2.11.1
  • Run at 2024-01-24 10:31:27

@jfy133 jfy133 marked this pull request as draft February 14, 2024 07:07
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jfy133 commented Apr 24, 2024

Gonna start AGAIN

@jfy133 jfy133 closed this Apr 24, 2024
@jasmezz jasmezz deleted the louperelo-nftest branch July 8, 2024 13:10
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@jfy133 @jasmezz @louperelo @nf-core-bot