Allow index files to be provided

[SusiJo]

Many thanks to contributing to qbic-pipelines/bamtofastq!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

PR checklist

• [ ] This comment contains a description of changes (with reason)
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] If necessary, add test data to testdata/
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
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[ggabernet]

Hi @SusiJo ,

thanks for the PR, I've added some comments. I did not see a clear reason so far for the failed tests but will investigate further.

[ggabernet]

@FriederikeHanssen could you also have a look at the PR whenever you have some time?

[FriederikeHanssen]

Looks great @SusiJo :) Thank you very much for contributing. If I am not mistaken, there is no test yet for the bai, right? Would be great to add it just to be sure it works at all times. From my side we can merge now though and I add the test, when I make the stats stuff optional.