Till Hartmann

Hmm, I'd be careful making the distinction between a "valid" file and a "parsable" one. One important point of a specification is to ensure that a file created by one...

I think I'd just modify the existing testcase to include this parameter, so we don't unnecessarily run the pipeline multiple times.

Hm, I think the rabbit may potentially have a point regarding the relative-ness of paths; but the thing is that some nextflow pipelines resolve their (relative) paths relative to the...

@fgvieira Any clue why the tests fail? Depending on run, we get permission errors on different binaries, e.g.,: [`ERROR test_wrappers.py::test_nextflow - PermissionError: [Errno 1] Operation not permitted: '/tmp/tmph3a872do/tmp8_ww334l/test/work/1a/290ea65c12de7b2287946c9c37d146/size_factors'`](https://github.com/snakemake/snakemake-wrappers/actions/runs/18349011296/job/52330726657?pr=4637#step:6:10051)