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Added nf-test for pipeline main.nf #25

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Merged
Parent: Release 1.1.0 - Resolution Road
merged 5 commits into from
Nov 27, 2023
Merged

Added nf-test for pipeline main.nf #25

merged 5 commits into from
Nov 27, 2023

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@kbestak
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@kbestak kbestak commented Nov 24, 2023

I've added the first 3 tests for the pipeline testing usage of modules in cases the second channel is provided or not, as well as if training subset creation works as expected.
Added test.config specifications.

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 necessary, also make a PR on the nf-core/molkart 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>).
  • CHANGELOG.md is updated.

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github-actions bot commented Nov 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9d4ead6

+| ✅ 158 tests passed       |+
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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
  • 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 ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-24 23:37:29

@FloWuenne FloWuenne mentioned this pull request Nov 27, 2023
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FloWuenne
FloWuenne reviewed Nov 27, 2023
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LGTM ⭐️!

@FloWuenne FloWuenne merged commit bc6f446 into dev Nov 27, 2023
@FloWuenne FloWuenne deleted the nf_test branch November 27, 2023 12:11
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@FloWuenne FloWuenne FloWuenne approved these changes

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@kbestak @FloWuenne