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Quick Start

Prerequisites

  • Docker installed on your system
  • Git for cloning the repository

Setup Steps

1. Clone the Repository

Download the repository:

git clone https://github.com/denisHanch/efsa_pipeline.git

Important!

Make sure that the pipeline data is in the data/inputs folder.

2. Start the Docker Container

./run_container.sh

Important!

Create a configuration file config.json based on data in data/inputs.

3. Run Input Validation

Running QC on the input data and processing data for the Nextflow pipeline to data/valid folder:

validate                              # default config (./data/inputs/config.json)
validate --config <path>              # custom config path

# Optional global option flags (config.json takes priority when both are set):
validate --threads <n|auto>           # number of threads, or 'auto'
validate --validation-level <level>   # strict / trust / minimal
validate --logging-level <level>      # DEBUG / INFO / WARNING / ERROR
validate --type <type>                # prokaryote / eukaryote
validate --force-defragment-ref       # unsupported workaround, at your own responsibility
                                      # ignored if force_defragment_ref is set in config.json

4. Execute the Pipeline

Start the pipeline:

nextflow run main.nf --max_cpu $(nproc) -params-file data/valid/validated_params.json -resume

Next Steps