diff --git a/README.md b/README.md index 9065bb3b8..20ad54cd3 100644 --- a/README.md +++ b/README.md @@ -1,38 +1,13 @@ -# ![nfcore/test-datasets](docs/images/test-datasets_logo.png) -Test data to be used for automated testing with the nf-core pipelines +# test-datasets: mcmicro -> ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)** +This branch contains test data to be used for automated testing with the [nf-core/mcmicro](https://github.com/nf-core/mcmicro) pipeline. -## Introduction +## Content of this repository +`samplesheets/markers-test.csv`: Markersheet file for minimal test
+`samplesheets/samplesheet-test.csv`: Samplesheet file for minimal test
+`samplesheets/markers-test_full.csv`: Markersheet file for full test
+`samplesheets/samplesheet-test_full.csv`: Samplesheet file for full test
-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. +### Test dataset origin -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) +The image files referenced in the samplesheets are human tonsil section 5 μm thick, imaged in four-channel immunofluorescence over three rounds of bleaching and re-staining with different antibodies. Published in https://doi.org/10.1038/s41592-021-01308-y (slide WD-75684-02). These image files each contain a 3 x 3 grid of overlapping four-channel image tiles with dimensions 220 x 180 pixels. The tiles were cropped from a single raw tile taken from one of the original data files. A Python script (https://github.com/labsyspharm/nf-core-test-datasets-build/blob/main/tonsil-cycif/tonsil-cycif.py) was written to extract the synthetic tile fields from an "interesting" region of the single raw tile, generate stage position metadata with random perturbations to approximate the behavior of a real-world microscope stage, and save the images and metadata as an OME-TIFF file. diff --git a/samplesheets/markers-test.csv b/samplesheets/markers-test.csv new file mode 100644 index 000000000..06726586f --- /dev/null +++ b/samplesheets/markers-test.csv @@ -0,0 +1,5 @@ +channel_number,cycle_number,marker_name +1,1,DNA 1 +2,1,Na/K ATPase +3,1,CD3 +4,1,CD45RO diff --git a/samplesheets/markers-test_full.csv b/samplesheets/markers-test_full.csv new file mode 100644 index 000000000..0dc5030b0 --- /dev/null +++ b/samplesheets/markers-test_full.csv @@ -0,0 +1,9 @@ +channel_number,cycle_number,marker_name +1,1,DNA_6 +2,1,ELANE +3,1,CD57 +4,1,CD45 +5,2,DNA_7 +6,2,ELANE7 +7,2,CD577 +8,2,CD457 diff --git a/samplesheets/samplesheet-test.csv b/samplesheets/samplesheet-test.csv new file mode 100644 index 000000000..3450b8fe2 --- /dev/null +++ b/samplesheets/samplesheet-test.csv @@ -0,0 +1,2 @@ +sample,cycle_number,channel_count,image_tiles +TEST1,1,4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif diff --git a/samplesheets/samplesheet-test_full.csv b/samplesheets/samplesheet-test_full.csv new file mode 100644 index 000000000..033f1ddee --- /dev/null +++ b/samplesheets/samplesheet-test_full.csv @@ -0,0 +1,5 @@ +sample,cycle_number,channel_count,image_tiles +TEST1,1,4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif +TEST1,2,4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif +TEST2,1,4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif +TEST2,2,4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif \ No newline at end of file