Run Nextflow inside Docker

[r0f1]

Hi,

I have the same problem as discussed here: #3782

I would like to run nextflow run from inside a webserver that is dockerized. However, the flag -d / -dockerize for nextflow run is gone now in the latest version of nextflow. The documentation says it is just depricated, but it is gone.

I found this article that suggests a solution to the problem by either 1) mounting /var/run/docker.sock or 2) using a special image.

How can I make either 1) or 2) work? Does nextflow allow me that kind of low-level access and/or forwards these additional command line flags?

[bentsherman]

I would just study how the dockerize option was implemented in Nextflow and take a similar approach:

nextflow/nextflow

Lines 226 to 237 in 973b031

	if [[ "$dockerize" ]]; then
	if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi
	NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets}
	mkdir -p "$NXF_ASSETS"
	exec docker run $detach --rm --net host \
	-e NXF_ANSI_LOG=false \
	-e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \
	-v /var/run/docker.sock:/var/run/docker.sock \
	-v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \
	nextflow/nextflow:$NXF_VER nextflow "${args[@]}"
	exit 1
	fi

It is just some Bash code to launch the Nextflow pipeline in a Docker image, with some extra options so that the task containers are launched in the host environment rather than within the Nextflow container. We removed it because it was difficult to maintain in a generic way, but as a custom solution it is feasible.