Verified Commit 8f9a3e6d authored by Laurent Modolo's avatar Laurent Modolo
Browse files

README.md: add tests section

parent aac63da9
......@@ -40,33 +40,33 @@ for example to initialise `file_handle` version `0.1.1`, run:
src/nf_modules/file_handle/0.1.1/docker_init.sh
```
To initialise all the tools:
```sh
find src/nf_modules/ -name "docker_init.sh" | awk '{system($0)}'
```
## Running the tests
To run tests we first need to get a trainning set
```sh
cd data
git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
cp data/tiny_dataset/fastq/tiny_R1.fastq data/tiny_dataset/fastq/tiny2_R1.fastq
cp data/tiny_dataset/fastq/tiny_R2.fastq data/tiny_dataset/fastq/tiny2_R2.fastq
cp data/tiny_dataset/fastq/tiny_S.fastq data/tiny_dataset/fastq/tiny2_S.fastq
nextflow src/nf_test.nf -c src/nf_test.config --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
cp tiny_dataset/fastq/tiny_R1.fastq tiny_dataset/fastq/tiny2_R1.fastq
cp tiny_dataset/fastq/tiny_R2.fastq tiny_dataset/fastq/tiny2_R2.fastq
cp tiny_dataset/fastq/tiny_S.fastq tiny_dataset/fastq/tiny2_S.fastq
cd ..
```
Explain how to run the automated tests for this system
### Break down into end to end tests
Explain what these tests test and why
Then to run the tests for a given tools run the following command:
```sh
src/nf_modules/<tool_name>/<tool_version>/tests/tests.sh
```
Give an example
```
### And coding style tests
Explain what these tests test and why
for example to run the tests on `Bowtie2` run:
```
Give an example
```sh
src/nf_modules/Bowtie2/tests/tests.sh
```
## Contributing
......
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