feat(modules_testdata_base_path): update guidelines for test data #2474
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jfy133
reviewed
Apr 26, 2024
Co-authored-by: James A. Fellows Yates <[email protected]>
maxulysse
commented
Apr 26, 2024
mashehu
approved these changes
May 3, 2024
| @@ -57,10 +57,10 @@ In contrast, if your module requires many tests, steps, or heavy CPU usage, you | |||
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| 11. The test data pull request requires a review to be merged. | |||
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| 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`: |
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| - 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) | |
| ``` |
| - 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)` | ||
| - 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. |
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@netlify /docs/contributing/test_data_guidelines