ExtractorFlow pipeline

Usage

See USAGE or run nextflow run main.nf --help

Singularity

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

Docker

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