Support for Docker ENTRYPOINTs

[Matt Dyer]

This is more of a feature request (or maybe I am missing an option somewhere), but it would be great to support containers that have defined entrypoints. The way that nextflow runs the container currently is by wrapping it in a shell script so it won't work.

process Foo{

     container 'Foo'

     """

     -h

     """

}

The container Foo has the entrypoint defined as 'foo' and the intent is to run 'foo -h' but when nextflow wraps things up it calls

docker run -i -v /Users/mattdyer/Documents/Programming/workflows:/Users/mattdyer/Documents/Programming/workflows -v $PWD:$PWD -w $PWD --name nxf-47cea6e1 Foo /bin/bash -ue /Users/mattdyer/Documents/Programming/workflows/.command.sh &> .command.out

Which takes the following shell script and runs it in the container.

#!/bin/bash -ue

-h

Really what I would like to is have nextflow run 

docker run -i -v /Users/mattdyer/Documents/Programming/workflows:/Users/mattdyer/Documents/Programming/workflows -v $PWD:$PWD -w $PWD --name nxf-47cea6e1 Foo -h &> .command.out

I apologize if I missed a flag that would allow this. If not, then just a feature request.

Best,

Matt

[Jimmy Jia]

The motivation here is that Docker best practices generally call for treating images as applications and containers as processes, rather than VMs and environments respectively.

Given that, it seems more idiomatic to put the wrapper scripts inside the images and just docker run them with a specified set of arguments, rather than passing in a script to run within the container.

[Paolo Di Tommaso]

Yes, the point is that a Nextflow process is supposed to execute a script, not a simple command line. 

For this reason the process code is wrapped into a script file and executed in the container when a Docker image is specified. 

However, I agree that this limits the ability of using existing containers. I'm opening a feature request to improve how Docker entrypoint is managed by Nextflow 

Cheers,

Paolo

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[Jimmy Jia]

Thanks! I think being able to integrate with application containers will make it much cleaner to wrap up applications in containers and use them as elements of a workflow.

Where do you track feature requests? Is it on GH issues?

[Paolo Di Tommaso]

Yes, we use Github but I haven't yet created the feature request. Feel free to contribute creating it :)

p

[Jimmy Jia]

Done: https://github.com/nextflow-io/nextflow/issues/33

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[Paolo Di Tommaso]

Thanks

p

[Paolo Di Tommaso]

Request for comments on supporting executable containers in Nextflow 

https://github.com/nextflow-io/nextflow/issues/33

Cheers,

p