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feat(modules_testdata_base_path): update guidelines for test data #2474

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feat(modules_testdata_base_path): update guidelines for test data #2474

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feat(modules_testdata_base_path): update guidelines for test data
maxulysse Apr 26, 2024
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maxulysse Apr 26, 2024
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6 changes: 3 additions & 3 deletions src/content/docs/contributing/test_data_guidelines.md
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Expand Up @@ -57,10 +57,10 @@ In contrast, if your module requires many tests, steps, or heavy CPU usage, you

11. The test data pull request requires a review to be merged.

12. Once you've had your pull request merged in into `nf-core/test-datasets`, make another PR into [nf-core/modules](https://github.com/nf-core/modules), to add your file as a new entry to the [`modules/tests/config/test_data.config`](https://github.com/nf-core/modules/blob/master/tests/config/test_data.config).
12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use refer to the newly uploaded file(s) for your test(s). Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. an example using the `fasta` file from `sarscov2`:
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12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use refer to the newly uploaded file(s) for your test(s). Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. an example using the `fasta` file from `sarscov2`:
12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can refer to the newly uploaded file(s) for your test(s). Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. an example using the `fasta` file from `sarscov2`:


- This only applies field-specific collections, `delete_me/` files are excluded from this, and raw github URLs should be used in tests.
- The 'key' for each URL should follow the style of the full file name with extensions but with underscores rather than full-stops e.g. `genome.fa.gz` would become `genome_fa_gz`.
- `file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)`
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- `file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)`
```groovy
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
```

- Note the file string corresponds to the directory structure of the modules repository.
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- Note the file string corresponds to the directory structure of the modules repository.
Note that the file string corresponds to the directory structure of the modules repository.


### Field specific guidance

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