Adding option for star aligner

[stephen-bin]

This update gives users options to choose the aligner to use (STAR/HISAT), via config.yaml file.

We have noticed higher mapping rates with STAR than with HISAT2 - when HISAT2 was originally implemented in rna-seq-pop, it was mainly for the purpose of speed. There are now indications that STAR may be better for SNP calling - for example, it is used in GATK best practices for RNA-Seq.

It will address issue #112

[sanjaynagi]

Hey @stephen-bin 👍

Thanks for the awesome pull request!!

I've just made some comments, mostly relating to replacing HISAT2 completely, rather than giving the user an option of doing both. Although this would be a good feature, Im trying to keep rna-seq-pop as simple as possible at the moment, to reduce the likelihood of users running into errors and so that its less work for me to maintain.

I've just set the github actions CI (continuous integration) to run, which will set up the repo in the cloud and run it on the test data, to see if the changes are functioning.

If you want to try and make those changes, then I can give more feedback :) Let me know if you have any questions

[stephen-bin]

You're very welcomed.

[sanjaynagi]

Hi @stephen-bin , just had a quick look at the recent changes. There should be no need for an aligner option in the config at all - users should not be able to choose the aligner - they are forced to use star. That should then simplify a lot of the implementation, there is no need for if else logic around the aligner.

Let me know if that makes sense, happy to discuss in more detail, or I can make some changes and show you what I mean :)

[stephen-bin]

Yes, well understood, you mentioned. I will update it and will reach out to you when I am done. It will also mean some other smks will be updated as well.