Anna Syme

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Run nextflow script with container

Install docker

Run nextflow script

nextflow run <your script> -with-docker [docker image]

e.g., if your process is seqkit stats $R1 > R1stats.txt

then run with: nextflow run -with-docker pegi3s/seqkit

Multiple docker containers

If each process needs a different container, add them in the config file.

Note: When putting the container names in here, rather than specifying in the run command as above, there may be a permission issue with some containers. see

make nextflow.config

add in:

process {
    withName:get_stats {
        container = 'nanozoo/seqkit'
    withName:get_stats2 {
        container = 'nanozoo/seqkit'
docker {
    enabled = true