See USAGE or run nextflow run main.nf --help
If you are on Linux, we recommend using the Singularity container to run ExtractorFlow
Run the command:
sudo singularity build singularity_extractorflow.sif singularity_extractorflow.def
Then you can start the pipeline using this command line:
nextflow main.nf --root=/path_to_your_data/ -with-singularity singularity_extractorflow.sif -resume
If you are on MacOS or Windows, we recommend using the Docker container to run ExtractorFlow.
You can build docker image using this command:
docker build -t extractor_flow .
nextflow main.nf --root=/path_to_your_data/ -with-docker extractor_flow:latest -resume