On a another workflow I got problems with running a similar container with Nextflow 22. There the Singularity container will fail to initialize the Conda environment. Not sure why this wasn't a problem in the past, but Nextflow uses singularity exec to execute the container. exec does not run the runscript section (by definition). Additionally, bash, as called by Nextflow (non-interactive, non-login) failed to load any of the initialization files (I tried even --init-file), so an initialization via /etc/bash.bashrc seemed not to be possible.
To-Do
Check whether we have the same problems here.
If so, see here how the fix is done for another workflow with a dedicated Singularity.def that has an %environment block.
Add singularity.runOptions = "--no-home" to the "singularity" block in the nextflow.config. This will prevent automatic loading of the .bashrc and the Conda initialization done there.
On a another workflow I got problems with running a similar container with Nextflow 22. There the Singularity container will fail to initialize the Conda environment. Not sure why this wasn't a problem in the past, but Nextflow uses
singularity exec
to execute the container.exec
does not run the runscript section (by definition). Additionally, bash, as called by Nextflow (non-interactive, non-login) failed to load any of the initialization files (I tried even--init-file
), so an initialization via/etc/bash.bashrc
seemed not to be possible.To-Do
Singularity.def
that has an%environment
block.