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nf-test init #73

Merged
merged 8 commits into from
Nov 24, 2022
Merged

nf-test init #73

merged 8 commits into from
Nov 24, 2022

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edmundmiller
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@edmundmiller edmundmiller commented Nov 24, 2022 •
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Closes #72

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/demultiplex 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).

@edmundmiller edmundmiller added this to the v1.1.0 milestone Nov 24, 2022
@edmundmiller edmundmiller self-assigned this Nov 24, 2022
@edmundmiller edmundmiller changed the base branch from master to dev November 24, 2022 02:13
@edmundmiller edmundmiller changed the title Nf test nf-test init Nov 24, 2022
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github-actions bot commented Nov 24, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f89ea6

+| ✅ 154 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: skip_tools

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-24 02:37:05

@nf-core nf-core deleted a comment from github-actions bot Nov 24, 2022
@edmundmiller
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@matthdsm Could you take a look at #74?

I also don't love how this came out. I'm debating splitting the tests up with the "tags" and maybe only running them if things change, but I'm okay with the slightly slower tests for the sake of not missing any breaking changes for now.

@edmundmiller edmundmiller marked this pull request as ready for review November 24, 2022 02:36
matthdsm
matthdsm reviewed Nov 24, 2022
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tests/pipeline/default/bases2fastq.nf.test
name "Test Bases2Fastq"
script "main.nf"

test("Should run without failures") {
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Shouldn't we keep the naming conventions from pytest?

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@sateeshperi and I thought it would be good to follow whatever nf-test generate spit out. But I'm guessing beyond the basic tests the naming will be out the window, and I don't want people to get caught up in following a convention when they could have an excellent name for a specific test.

Something we can circle back around to, though!

matthdsm
matthdsm approved these changes Nov 24, 2022
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Tests pass, LGTM!

@edmundmiller edmundmiller merged commit 8a5c1e9 into dev Nov 24, 2022
@edmundmiller edmundmiller deleted the nf-test branch November 24, 2022 15:22
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