Clean work dir without sudo

[akotlar]

nextflow clean -f , or indeed manual rm -rf /path/to/work/dir fails because it appears that any of the files that were generated within a docker container are "root". Using "sudo" is a nonstarter, since that would prevent the command from running headless.

Presumably, if I could issue the rm -rf command from within a nextflow process that is executed in Docker after all outputs are copied to the --output directory, I could get around this issue, but I cannot figure out how to do this. Any help would be appreciated.

[colindaven]

I would use a singularity or apptainer container built from your Dockerfile or docker container instead, that way you can avoid this problem. Running anything which can generate files as root on a critical shared machine is not good practice - which is why many hpcs do not allow docker.

[pditommaso]

Also, I believe, podman does much better to address this problem

[akotlar]

Cool, thanks guys