Problem setting singularity cache dir

[Edoardo Giacopuzzi]

Hi,

I'm trying to properly set up singularity cache directory in the nextflow configuration for my pipeline so that images downloaded from a repository go to a specific folder, but I can get it to work as expected.

In my configuration I have

singularity: {

  cacheDir: '/my/cache/location/'

}

When I run the pipeline the images pulled from the remote repository are correctly saved in the specified location, but it seems that temporary files are created anyway in the default singularity cache dir ($HOME/.singularity). This causes issues since the space available for the home folder is limited in my cluster. Basically, the pipeline crashes at some point since unable to download new containers due to the storage quota exceeded.

I've tried to add this to edit my configuration adding some env variables 

singularity: {

  cacheDir: '/my/cache/location/'

}

env {

  SINGULARITY_CACHEDIR = "/location/for/cache"

  SINGULARITY_TMPDIR = "/location/for/tmp"

}

But the result is the same (final images downloaded to the singularity.cacheDir, but data also in $HOME/.singularity). 

Any suggestion on how to set configuration properly so that singularity would only write data in the specified location doing nothing in the home folder?

Thanks!

[Paolo Di Tommaso]

The `env` scope it's only for tasks executed by NF not for configuring nextflow itself. Therefore the singularity variables needs to be defined in the host environment. 

p

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