When using option -d .test instead of -d ., apptainer doesn't find the expected files as they are relative to the .test dir.
In other words, these lines in the apptainer definition contain invalid paths due to prefixed ../
%files
../workflow/envs/get_genome.yaml /conda-envs/68fc50fd41aeaa780499c43b4b87783e/environment.yaml
../workflow/envs/simulate_reads.yaml /conda-envs/19ffc51f5e6e8f8eabfd705039b94e9f/environment.yaml
../workflow/envs/validate_genome.yaml /conda-envs/fbaefa4f07b727428a82883e7cdbc88b/environment.yaml
When using option
-d .testinstead of-d ., apptainer doesn't find the expected files as they are relative to the.testdir.In other words, these lines in the apptainer definition contain invalid paths due to prefixed
../