Run with docker & Singularity

Docker

• Prepare input files as mentioned earlier.
• Modify the docker.config in mandatory section.
• Install docker and download the latest circPipe build

docker pull bioinformatist/circPipe

• Run circPipe using the following command:

nextflow -c docker.config run main.nf

Singularity

• Prepare input files as mentioned earlier.
• Use a Docker image with Singularity by adding the --with-singularity option followed by the image path (--with-singularity docker://???????)

nextflow run main.nf --with-singularity docker:????????????

• Alternatively, users can also set the following parameters into the nextflow.config file:

singularity.enabled = true
process.container = "docker:???????????"