From cb4179ab057ab285e840f9093a7963820034bd4c Mon Sep 17 00:00:00 2001 From: Quentin Blampey Date: Wed, 28 Jan 2026 10:52:46 +0100 Subject: [PATCH 1/3] adding toy samplesheet (synthetic data) --- samplesheet/toy.csv | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 samplesheet/toy.csv diff --git a/samplesheet/toy.csv b/samplesheet/toy.csv new file mode 100644 index 000000000..2950c1938 --- /dev/null +++ b/samplesheet/toy.csv @@ -0,0 +1,2 @@ +sample,data_path +sample_name,https://github.com/nf-core/test-datasets/blob/sopa/samplesheet/toy.csv From cb1fb3a3b78e2b7a025ffcc3cd358246c57f13e6 Mon Sep 17 00:00:00 2001 From: Quentin Blampey Date: Wed, 28 Jan 2026 16:35:52 +0100 Subject: [PATCH 2/3] REDME update --- README.md | 36 +++--------------------------------- 1 file changed, 3 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index 9065bb3b8..a3f3db6a1 100644 --- a/README.md +++ b/README.md @@ -1,38 +1,8 @@ # ![nfcore/test-datasets](docs/images/test-datasets_logo.png) Test data to be used for automated testing with the nf-core pipelines -> ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)** +## Test data and samplesheets for Sopa -## Introduction +Some samplesheets are available under the `samplesheet` directory: -nf-core is a collection of high quality Nextflow pipelines. This repository contains various files for CI and unit testing of nf-core pipelines and infrastructure. - -The principle for nf-core test data is as small as possible, as large as necessary. Please see the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines) for more detailed information. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data. - -## Documentation - -nf-core/test-datasets comes with documentation in the `docs/` directory: - -01. [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md) -02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md) - -## Downloading test data - -Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use. - -```bash -git clone --single-branch --branch -``` - -To subsequently clone other branches[^1] - -```bash -git remote set-branches --add origin [remote-branch] -git fetch -``` - -## Support - -For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging). - -[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856) +- `toy.csv`: a toy samplesheet (under the hood, Sopa will create a synthetic dataset). From baebf684ac539cb83eb32fa24fbd76f51c736b13 Mon Sep 17 00:00:00 2001 From: Quentin Blampey Date: Wed, 28 Jan 2026 16:59:56 +0100 Subject: [PATCH 3/3] add description and link to sopa.io.toy_dataset --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a3f3db6a1..d1876ac3f 100644 --- a/README.md +++ b/README.md @@ -5,4 +5,4 @@ Test data to be used for automated testing with the nf-core pipelines Some samplesheets are available under the `samplesheet` directory: -- `toy.csv`: a toy samplesheet (under the hood, Sopa will create a synthetic dataset). +- `toy.csv`: a toy samplesheet (under the hood, Sopa will create a synthetic dataset via [`sopa.io.toy_dataset`](https://gustaveroussy.github.io/sopa/api/readers/#sopa.io.toy_dataset)). This dataset is composed of two spatial elements (an image and a transcript dataframe) representing cells generated uniformly in a square.