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nextflow run <your script> -with-docker [docker image]
e.g., if your process is seqkit stats $R1 > R1stats.txt
then run with:
nextflow run main.nf -with-docker pegi3s/seqkit
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 https://github.com/nextflow-io/nextflow/issues/1295
make nextflow.config
add in:
process {
withName:get_stats {
container = 'nanozoo/seqkit'
}
withName:get_stats2 {
container = 'nanozoo/seqkit'
}
}
docker {
enabled = true
}