Identification performance comparison Requirements Java (version depends on Nextflow) Nextflow Docker make Usage Build and download the Docker images: make docker-imgs Run the workflows nextflow run -profile docker src/main.nf --raws <FOLDER_WITH_RAW_FILES> ... Development / Contribution Nextflow is going into src/* Each process should use a container Make sure to put the each container download or build into the Makefile Python scripts are going into bin/ with the shebang #!/usr/bin/env python. Make it executable. Python dependencies are going into requirements.txt Any binary dependency for the Python Docker container are is going into environment.yml