/lrgasp-challenge-3_benchmarking_workflow

Primary LanguageNextflow

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
  1. 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
  1. Materialize both the containers and datasets needed by the LRGASP test:
cd LRGASP
bash ./materialize-data.sh
  1. Run the tests from LRGASP example
cd ../..
./test_VRE_NF_RUNNER.sh LRGASP