Francesco Tabaro

Sure! So, SalmonTE runs a Snakemake process after starting up. Snakemake creates lock files in the working directory it is running. This is to prevent other Snakemake processes to mess...

The other way. SalmonTE fails to start because it finds the lock of the outer pipeline.

One option could be to support Snakemake's `--unlock` option from SalmonTE top level scripts: e.g. `salmonTE quant [...] --no-lock`

I think there should be a switch to tell Snakemake whether to cache or not the given path.

Here is a possible workaround: https://github.com/snakemake/snakemake/issues/1805#issuecomment-1851506675

The issue was closed upstream: pepkit/peppy#420