Singularity does not automatically bind current working directory

[kubu4]

As noted in Issue #9 , this can be inelegantly solved by the user editing the Singularity system config file and then starting the pipeline.

However, I think the pipeline should automatically bind the working directory. This is especially important for users who do not have permissions to allow them to edit the Singularity system config file.

[bio15anu]

Thanks very much for the investigatory work! This looks like it is system-specific and so only relevant on a case-by-case basis depending on how singularity has been configured and installed for each user.

I think in your case the best solution would be to create a new configuration file called config in your nextflow system directory (usually ~/.nextflow) and in there add the following options:

singularity {
autoMounts = true
runOptions = "--bind /home/shared/8TB_HDD_01"
}

These settings will then apply globally to all Nextflow pipelines run by you on your system which make use of singularity, without need to edit the /etc/singularity/singularity.conf file.

This is based on the troubleshooting from nf-core that you found, and the singularity config scope here:
https://www.nextflow.io/docs/latest/config.html#config-singularity

and the steps in singularity manual here:
https://docs.sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html#user-defined-bind-paths

[kubu4]

Thanks for the follow up.

Is there anyway to automate this process where the current working directory could be added as a binding, upon initiation of the pipeline?

If other users try to run this pipeline in a different directory on this computer, then we'll constantly need to customize config files. Our lab has a wide range of user expertise and troubleshooting and/or customizing config files might be beyond the abilities of some members.

[bio15anu]

Yes, sure thing. You can change the runOptions line to e.g. "--bind ${launchDir}" and then in this case the path /home/shared/8TB_HDD_01/sam/analyses/epidiverse-wgbs-text would be automatically passed to the Singularity launcher.

You can then share the config file with all your users, who should save it as $HOME/.nextflow/config (not nextflow.config as I said originally above - my mistake, I edited it now). The config will apply globally and the path will change dynamically depending on where exactly in the file system each user starts the pipeline from.