Describe the bug
some container platform (e.g. Singularity) do not always run as "root" within the container.
this prevents writing into resource/ e.g. when indexing reference sequence
see:
To Reproduce
- V-pipe used with a virus base config (with built-in reference in
resources/)
- Singularity configured to pass-through username.
- rule
ref_bwa_index crashes as the reference FASTA in resources/ belongs to root, not to the username that gets passed through.
Expected behavior
- V-pipe should index the reference in
resource/