Chapter 4 Execution

  1. Clone the repo to your machine
git clone https://github.com/bio-TAGI/Hackathon.git
cd Hackathon
  1. Create and activate the virtual environment
conda env create -f nextflow_conda_env.yml
conda activate nextflow
  1. Run the wokflow with default parameters.
cd Nextflow
nextflow run main.nf
  1. If you had to stop the workflow run, or if some error occurred, you can always resume the execution as follows:
nextflow run main.nf -resume
  1. Specifying parameters from the command line
nextflow run main.nf --param1 value1\
--param2 value2\
--paramn valuen # these are generic names, not actual parameters for the pipeline