Description of the bug

The basicpy container puts pre-fetched bioformats java artifacts in /tmp and sets HOME=/tmp so maven finds them there. However when using apptainer (a.k.a. singularity) with the config option mount tmp = yes, the host system's /tmp is bind-mounted into the container and masks these artifact directories.

Furthermore, apptainer preserves $HOME from the calling environment by default which will require other workarounds in the nextflow config. Or there may be a different mechanism for telling maven where to find its artifacts.

Command used and terminal output

Relevant files

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System information

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