Hi all - I have what I hope is a simple (ish) question. We are noting an issue with one of the tools our pipeline (scnanoseq) implements when it is executed with NextFlow. This is linked to the behavior of not mounting the directory and this particular tool writes in small directory at

$HOME

, and there is currently no parameter within the tool to change this location. We can get around this by enabling the following before the

nextflow run

command -

export NXF_SINGULARITY_HOME_MOUNT=true

. This solves the issue, but I am unsure if there is way for us to streamline this process to users? Or is this just a matter of adding this need in the docs (I noted pixelator has done at the README: https://github.com/nf-core/pixelator)

Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable

NXF_APPTAINER_HOME_MOUNT

or

NXF_SINGULARITY_HOME_MOUNT

to

true

in the machine from which you launch the pipeline.

Any feedback is appreciated on what is best for the nf-core community.

That won't work, this is a Nextflow configuration env variable, so needs to be in the environment before Nextflow itself loads

Ah yes you're right! I didn't see it was a nextflow env 😁

I don't completely understand why the external home directory needs to be available to be honest

The tool is IsoQuant, and related to this: https://github.com/ablab/IsoQuant/blob/fd6407d6f79e9351daf845dc3d575fc4292e94a6/isoquant.py#L696 We will open a feature request to make this section into a param at least and in the longer run hopefully we can remove this requirement. This is not the only tool that does this. BLAZE in our pipeline also does it (same request / PR will go in the future).

aha, so it can see your home directory but not write to it. gotcha

correct

we have the same issue in crisprseq, we couldn't find a good solution apart from running the pipeline with

export NXF_SINGULARITY_HOME_MOUNT=true

How irritating. Funny that this thread was almost exactly the same as above with beforeScript 😅

Sounds good will do! If we cannot find a resolution, we will move forward with adding a warning in the documentation as @Júlia Mir has done along with others so we can move forward with a first release (but either way, I will be on the look-out on this for a more permanent solution). Thanks so much all for the feedback here.

Thanks, sounds good! Yes it'd be nice to have a solution, sounds like several pipelines would benefit..

Ok - I seem to have found the solution before contacting the other channel (may still post there out of curiosity and see what they think). Digging through the docs I saw https://www.nextflow.io/docs/latest/process.html#containeroptions So, adding

containerOptions "--bind ${task.workDir}:/home"

to IsoQuant’s process now adds the directory it writes to nextflow’s

work

dir (e.g.:

scnanoseq/work/lianov/76/6dac21..../.config/IsoQuant

) So that seems to do the trick for me. @Júlia Mir Is this something you have tried?

Oh nice! I will try it out too 🙂

@Júlia Mir: A quick update. In the above, I had forgotten that Docker’s binding option is different from Singularity and Apptainer. So if you proceed with that, the above example is over-simplistic. It should look more like this to make it work across the 3 containers that I have checked (Apptainer, Singularity and Docker):

containerOptions "${workflow.containerEngine == 'docker' ?
    '--mount type=bind,source=' + task.workDir.toString() + ',target=/home' :
    '--bind ' + task.workDir.toString() + ':/home'}"

That being I did cross post this in #CKDDD9JB0 as suggested by Phil to see if we had additional options to work with (https://nfcore.slack.com/archives/CKDDD9JB0/p1724879621376119). One solution that also works and I think more simple than the above is in the reply - to add

export HOME=\$(pwd)

to the

script

section of the process. This seemed to work fine on my quick test and was suggested to be the better solution for pipeline maintainers. I am doing a few other tests, but don’t see why this shouldn’t work across the board (and this way we are not dealing with container specific syntax).