Deal with relative paths in input tables

In these tables the paths of where the samples are are relative and not absolute. I want to start running Snakemake on the level where it is, so these relative paths are not correct anymore. @boersch, @kanitz can you help on how we can obtain absolute paths? Is there even such a possibility? How would we test this on CI/CD then ? Otherwise can we just keep the relative paths in relation to the level of Snakefile? @boersch can you show how this test case paths look like in the samples table?

I have applied the workdir option in Snakemake config to move the path to the level of Snakefile when calling it from within the tests and so far the only issue is that I had to manually change the paths in the samples.tsv