Run with docker & Singularity

Docker

• Prepare input files as mentioned earlier.
• Pull or build the image Users could either pull the pre-built image from DockerHub, using the following command:

docker pull ???alesssia/???circdocker???

or build a local image using the file Dokerfile in the ??circdocker?? folder.

docker build -t yampdocker .

• Use the image by adding the -with-docker option followed by the image name (???alesssia/???circdocker, if pulled, or ???circdocker, if built), that is, with the following command, which assumes a pulled image:

nextflow run main.nf  -with-docker ???alesssia/???circdocker

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

docker.enabled = true
process.container = '???alesssia/???circdocker:latest'

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:???????????"