Simple pipeline level nf-tests #1272
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Additions: - Runs simple tests for workflows - Directly replaces existing tests in .github/workflows - No checks for outputs or contents
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maxulysse
approved these changes
Mar 21, 2024
maxulysse
reviewed
Apr 8, 2024
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tests/tests/default/?
why not tests/default/
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The reason is to keep it tidy. You have a primary tests/ folder with tests, lib and other stuff (e.g. conf).
tests
├── lib
│ └── UTILS.groovy
├── nextflow.config
└── tests
├── default
│ ├── main.nf.test
│ └── main.nf.test.snap
├── featurecounts
│ └── main.nf.test
├── min_mapped_reads
│ └── main.nf.test
├── remove_ribo_rna
│ └── main.nf.test
├── skip_qc
│ └── main.nf.test
└── skip_trimming
└── main.nf.test
Without it, you would end up with this which I think is messy:
tests
├── default
│ ├── main.nf.test
│ └── main.nf.test.snap
├── featurecounts
│ └── main.nf.test
├── lib
│ └── UTILS.groovy
├── min_mapped_reads
│ └── main.nf.test
├── nextflow.config
├── remove_ribo_rna
│ └── main.nf.test
├── skip_qc
│ └── main.nf.test
└── skip_trimming
└── main.nf.test
But I could be convinced otherwise.
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We could move the tests/nextflow.config file into tests/config/nextflow.config for consistency?
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I'd go with:
tests
├── default.main.nf.test
├── default.main.nf.test.snap
├── featurecounts.main.nf.test
├── lib
│ └── UTILS.groovy
├── min_mapped_reads.main.nf.test
├── nextflow.config
├── remove_ribo_rna.main.nf.test
├── skip_qc.main.nf.test
└── skip_trimming.main.nf.test
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Oh bother automerge was too quick.
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The role of this PR is to open a discussion on how to organise and run pipeline level tests.
I have directly replaced the existing tests with simple tests which change a single parameter and check for succesful completion, no snaps, no hashes etc. That can come later.
In this PR I'd like to discuss test organisation, naming, handling etc. I've tried my best to make it simple and easy to understand while being flexible enough to work efficiently, let me know what you think.