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

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System information

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