Add support for using GFF instead of GTF

[milos7250]

I thought it would be a nice addition to have the option to use GFF files as well as GTF files when specifying references. I was inspired by the rnaseq pipeline and added the conversion from GFF to GTF.

I have tried this on a small dataset using barley genome and it worked well. For a complete PR I think this would require adding one test where a GFF is supplied instead of a GTF.

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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[milos7250]

I believe I have now included everything that is mentioned in the contributing guidelines, except writing a new test for this feature. As this would involve another PR for including more files in the test repository, I will hold on from doing that until more people agree that it is necessary.

I cancelled the tests for the previous commit, as it felt wasteful to run the same tests after only updating the changelog.

[nf-core-bot]

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