Simple pipeline level nf-tests #1272
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Additions: - Runs simple tests for workflows - Directly replaces existing tests in .github/workflows - No checks for outputs or contents
|
maxulysse
approved these changes
Mar 21, 2024
maxulysse
reviewed
Apr 8, 2024
There was a problem hiding this comment.
tests/tests/default/?
why not tests/default/
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
We could move the tests/nextflow.config file into tests/config/nextflow.config for consistency?
There was a problem hiding this comment.
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
There was a problem hiding this comment.
Oh bother automerge was too quick.
|
We made it! 🥳 |
11 tasks
This pull request was closed.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.