Check that indices can be specified as expected

[grst]

Description of the bug

Specifying indices should work as expected from a nf-core pipeline, i.e.

• igenomes should be respected
• it shall be possible to specify pre-computed indices and they shall be actually used
• it shall be possible to generate indices from fastq/gtf otherwise.

There are a couple of issues related to that and it's probably best to address them all in one go and add tests where it makes sense.

Related issues:
#390
#339
#345

Command used and terminal output

No response

Relevant files

No response

System information

No response

[kopichris]

Happy to look into this if the issue is still open 👍

[grst]

It would be great if you could take a look, but it's better to wait until #369 is merged because @fmalmeida already made some changes to this (but without the aim to address this entirely).

If you already want to get startet, you could also try out the branch from #369 - It would anyway be good to get some additional feedback on this because it entails quite some changes.