A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Any idea what these singularity errors here are about: <https://github.com/nf-core/proteinfamilies/actions/runs/31109208095/job/92642599648?pr=183|github.com/nf-core/proteinfamilies/…/92642599648?pr=183>
```&gt; Command error:
      &gt;   WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_TASK_WORKDIR as environment variable will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead
      &gt;   WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
      &gt;   ERROR  : Failed to create container process: Operation not permitted```


This snippet in /nf-test/action.yml seems to have fixed it!
```with:
        # Action defaults to 1.1.2, which predates the AppArmor profile Ubuntu 24.04 runners
        # need for unprivileged user namespaces ("Failed to create container process").
        apptainer-version: 1.5.3```
Thank the bots. Leaving it like this until an updated template arrives.