Singularity allow "--userns"

[KeyTals]

Hello,

We need provide "-u" or "--userns" while we run singularity on server installation. Is there any way to provide "-u" while running singularity mode of pipeline?

Keyur

[replikation]

hi @KeyTals yes, it is possible to provide additional container flags to singularity.

Edit: This works:

# create the configuration file
echo "singularity.runOptions = '--userns'" > singularity.config

# merge the config into poreCov, e.g.:
nextflow run replikation/poreCov -c singularity.config   --fastq <stuff> -profile local,singularity -r 0.7.13

[KeyTals]

Thank you very much for the quick reply. Now i am not getting the -u specific error.

Keyur

[replikation]

• nice, please report back if it everything works, I would like to add this to the readme as "troubleshooting" for others

[KeyTals]

Pipeline works fine.

Thanks,
Keyur