Port old test-data guide to new layout

sites/docs/src/content/docs/developing/testing/advanced.md

@@ -2,7 +2,7 @@
 title: Advanced techniques
 subtitle: Write complex assertions
 shortTitle: Advanced assertions
-weight: 3
+weight: 4
 ---
 
 Advanced assertion patterns handle complex testing scenarios where standard snapshots are insufficient.

sites/docs/src/content/docs/developing/testing/assertions.md

@@ -2,7 +2,7 @@
 title: nf-core guidelines for assertions
 subtitle: Write test assertions
 shortTitle: Assertions
-weight: 2
+weight: 3
 ---
 
 nf-core guidelines for assertions:

sites/docs/src/content/docs/developing/testing/ci-runners.md

@@ -2,7 +2,7 @@
 title: CI runners
 subtitle: Configure RunsOn and fix CI disk space issues
 shortTitle: CI runners
-weight: 4
+weight: 5
 ---
 
 nf-core uses [RunsOn](https://runs-on.com/) for self-hosted AWS runners that run GitHub Actions.

sites/docs/src/content/docs/developing/testing/overview.md

@@ -56,6 +56,11 @@ Both directives work within their defined scope: either for all tests within the
 
 nf-test replaces paths in snapshots with a unique fingerprint (MD5 sum by default) to ensure file content consistency.
 
+:::note
+nf-core pipelines, modules, and subworkflows should specify input files from nf-core/test-datasets.
+See the [test-data](./test-data.md) page for more information.
+:::
+
 ### Asserting channel item presence with `contains`
 
 Use Groovy's `contains` and `collect` methods to assert the presence of items in channel output.
@@ -132,6 +137,7 @@ The nf-test documentation provides additional information on:
 
 Learn how to write effective test assertions following nf-core guidelines:
 
+- [Test data](./test-data) covers how to find and prepare test-data files
 - [Writing assertions](./assertions.md) covers nf-core guidelines and common assertion patterns
 - [Advanced techniques](./advanced.md) covers complex patterns and troubleshooting
 - [CI runners](./ci-runners.md) covers RunsOn configuration and CI disk space issues

sites/docs/src/content/docs/developing/testing/test-data.md

@@ -0,0 +1,111 @@
+---
+title: Test data
+subtitle: Finding and adding test data for CI testing
+shortTitle: Test data
+weight: 2
+---
+
+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.
+This guide explains how to find and upload new test data.
+
+## Modules and subworkflows
+
+### Reusing existing test data
+
+When setting up tests for a nf-core component, test data files should be reused as far as possible.
+
+:::tip
+If a small test data file for your module can be quickly generated by an upstream module, do not add the input file to the test data.
+Run the upstream module in the test for your module using the [nf-test `setup` method](https://www.nf-test.com/docs/testcases/setup/?h=setup).
+:::
+
+Test data for modules and subworkflows are stored on the [`modules`](https://github.com/nf-core/test-datasets/tree/modules) branch of nf-core/test-datasets.
+The branch is approximately structured as follows:
+
+```tree
+data/
+├── delete_me/
+│   └── <tool name>/
+│        └── <test data file>
+├── generic/
+│    └── <format>/
+│        └── <test data file>
+└── <research domain>/
+    └── <technology or analysis>/
+    │    └── <format>/
+    │        └── <test data file>/
+    └── <species>/ ## Bioinformatics only
+        └── <technology or analysis>/
+            └── <format>/
+                └── <test data file>/
+```
+
+Existing nf-core test data can be explored using nf-core/tools.
+
+```bash
+nf-core test-datasets search --branch modules
+```
+
+Type in the search bar keywords such as for file formats or extensions to find potentially relevant files.
+To get more information about the context of the data, see the [nf-core/test-datasets README](https://github.com/nf-core/test-datasets/tree/modules#data-description) file.
+
+Selecting a file to print different variants of URLs to the test data file for use in tests.
+
+### Uploading new data
+
+If you cannot generate [test data on the fly quickly](https://www.nf-test.com/docs/testcases/setup/?h=setup), or reuse existing data, you can upload new compliant test data to the `modules` branch.
+
+If you need to create a derivative file, use existing test data as a source.
+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.
+
+:::danger
+Do not clone the nf-core/test-datasets repository: it is extremely large and will take a long time to download.
+If a local copy is required, we highly recommend using [single-branch clones](https://github.com/nf-core/test-datasets#downloading-test-data).
+:::
+
+1. Verify your new test-data file complies with the [nf-core test-datasets specifications](../../specifications/test-data/overview.md).
+2. Fork the nf-core/test-datasets repository including all branches.
+3. Upload to the `modules` branch on your fork in a suitable location.
+   - (Recommended) Use the GitHub website upload function.
+   - If you are unsure of the suitable location, ask on the nf-core [#test-data](https://nfcore.slack.com/archives/C02L5UB4Y9G) Slack channel.
+4. Edit the README of the `modules` branch to add a short entry describing the new test data file.
+   - Include as much information as possible to support reconstruction of the file (for example, original source accession numbers or URLs, tool name and version used to generate).
+   - (Optional) If a description requires more than one or two sentences Additionally add a dedicated README markdown file alongside the test-data file itself.
+5. Open a pull request and request a review on the nf-core [#request-review](https://nfcore.slack.com/archives/CQY2U5QU9) Slack channel.
+
+### Research domain specific guidance
+
+#### Biology
+
+Avoid adding test data of new organisms as far as possible, and reuse existing files.
+
+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.
+
+## Pipelines
+
+Each official nf-core pipeline has a dedicated branch on the test-datasets repository, for example, [nf-core/rnaseq](https://github.com/nf-core/test-datasets/tree/rnaseq).
+
+Reusability principles are less strict for pipeline test data.
+Test data should not be reused across pipelines for stability purposes.
+Reusing test data from modules for pipeline tests is possible due to the greater stability of these files.
+
+A pipeline-specific nf-core/test-datasets branch will generally consist of:
+
+- Small raw input files (for example, FASTQ, FASTA etc. for bioinformatics)
+- Samplesheets
+
+### Adding new test data
+
+1. Verify your new test-data file complies with the [nf-core test-datasets specifications](../../specifications/test-data/overview.md).
+2. Fork the nf-core/test-datasets repository.
+3. Upload to the dedicated pipeline branch in a suitable location.
+   - (Recommended) Use the GitHub website upload function.
+4. Edit the README of the dedicated pipeline branch describing how the file was generated.
+   - 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.
+
+## Related documentation
+
+- [nf-core/test-datasets](https://github.com/nf-core/test-datasets/)
+- [Test data specifications](../../specifications/test-data/overview)