bowtie2 added

[DOH-HNH0303]

With samtools included to immediately convert sam files to bam files

[kapsakcj]

Hi Holly, thanks for the PR. This is an essential bioinfo tool that is missing from our collection.

I was able to build the docker image successfully and was able to align some single end sars-cov-2 reads to it's assembly, followed by samtools view [...] & samtools sort [...] which ran as expected. Everything checks out on my end ✔️

I have some minor suggestions for the dockerfile that I would like to put forward before we merge the PR and build the image on dockerhub and quay. I'll make comments on the dockerfile & README.md

[kapsakcj]

OK, I made my comments. Please let me know if you have any questions or if I can clarify anything.

Thank you!

[DOH-HNH0303]

Changes were made as suggested and tested locally. Thanks for your feedback!

[kapsakcj]

Awesome, thank you. Tested out great on my end again. I will merge and push to dockerhub and quay.

[kapsakcj]

The docker image is now available on dockerhub and quay. Thank you for the PR!

https://hub.docker.com/r/staphb/bowtie2/tags?page=1&ordering=last_updated

https://quay.io/repository/staphb/bowtie2?tab=tags