Port old test-data guide to new layout#4283
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As mentioned on Slack, it looks good to me! Cheers! |
mashehu
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| 3. Upload to the dedicated pipeline branch in a suitable location. | ||
| - (Recommended) Use the GitHub website upload function. |
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why the recommendation for using the web GUI?
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So you don't have to clone the repo 😅
christopher-hakkaart
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Jul 12, 2026
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I've added some very low-level suggestions. Consider them optional. Otherwise I think it looks good.
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| nf-core has a central repository on [nf-core/test-datasets](https://github.com/nf-core/test-datasets) containing small data files for testing of nf-core components and pipelines. |
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| nf-core has a central repository on [nf-core/test-datasets](https://github.com/nf-core/test-datasets) containing small data files for testing of nf-core components and pipelines. | |
| nf-core maintains a central repository on [nf-core/test-datasets](https://github.com/nf-core/test-datasets), which contains small data files for testing nf-core components and pipelines. |
| For example, if you need to test a new bioinformatic short-read aligner that requires a genome file index, use an existing `genome.fasta` file on nf-core/test-datasets to generate the index, rather than using your own reference genome. | ||
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| :::danger | ||
| Do not clone the nf-core/test-datasets repository: it is extremely large and will take a long time to download. |
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| Do not clone the nf-core/test-datasets repository: it is extremely large and will take a long time to download. | |
| Do not clone the nf-core/test-datasets repository. It is extremely large and will take a long time to download. |
| Avoid adding test data of new organisms as far as possible, and reuse existing files. | ||
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| SARS-CoV-2 and _Homo sapiens_ (Chr 21) are the best supported organisms and should be used where possible. | ||
| If a new organism is absolutely required for a tool, first propose the addition on the [#test-data](https://nfcore.slack.com/archives/C02L5UB4Y9G) Slack channel. |
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| If a new organism is absolutely required for a tool, first propose the addition on the [#test-data](https://nfcore.slack.com/archives/C02L5UB4Y9G) Slack channel. | |
| If a new organism is absolutely required for a tool, propose the addition on the [#test-data](https://nfcore.slack.com/archives/C02L5UB4Y9G) Slack channel. |
| - Include as much information as possible that could allow reconstruction of the file (for example, original source accession numbers or URLs, tool name and versions used to generate). | ||
| 5. Open a pull request and request a review on the nf-core [#request-review](https://nfcore.slack.com/archives/CQY2U5QU9) Slack channel. | ||
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| ## Related documentation |
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| ## Related documentation | |
| ## Learn more |
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As reported on Slack by @pmoris , we are missing the old guide for nf-test datasets.
It was inadvertently dropped from the original porting as it was clustered in a big batch of files that we decided against porting for completeness reasons.
I have retrieved this specific file and tried to clean it up as far as possible to remove more 'specifications' like text and kept it strictly as a guide, including against the style guide.
I placed it in the existing 'testing' section because even if it's not necessarily nf-test related, it is intrinsically involved and I feel it would be the most likely place a user would look to find information bout it.
(Already LLM-assisted reviewed against style guide by Claude Haiku 4.5)
@netlify /docs/developing/testing/test-data