Redesign rule wiring

@kanitz @gypas I realised that there is an issue with the structure of the names in the snakemake pipelines

I wanted to make these indexes depending on the organism and the index size , independent of the sample, but I never propagated these values in the output of the snakemake rules, leading to many limitations.

I propose that I now include all the wildcards somehow in the output name This means we have to fix the md5sums in the test_integration_workflow