LRGASP challenge 3 mouse OpenEBench workflow

The workflow used to run the LRGASP challenge 3 mouse docker in the OpenEBench VRE executor.

The repository includes several files:

1. Example input dataset lrgasp-challenge-3_full_data folder.
2. config.json: the configuration file of the workflow. It contains different elements under arguments, including the git repository of the workflow, the specific commit to try, the community id, a participant id and the parameter with the challenges to compute.
3. in_metadata.json: define the directories of the input files. The file declares the input files' detail locations inside the config.json.
4. materalize-data.sh: materialize the datasets needed in pre-defined relative paths
5. materialize-containers.sh: building the needed containers for LRGASP workflow

Usage

1. Install OpenEBench VRE executor and go to the tests folder

cd vre-process_nextflow-executor/tests

2. Clone the LRGASP mouse workflow repository and rename the folder to LRGASP

git clone https://github.com/TianYuan-Liu/lrgasp-challenge-3_benchmarking_workflow.git
mv lrgasp-challenge-3_benchmarking_workflow LRGASP

3. Materialize both the containers and datasets needed by the LRGASP test:

cd LRGASP
bash ./materialize-data.sh

4. Run the tests from LRGASP example

cd ../..
./test_VRE_NF_RUNNER.sh LRGASP