Update index workflow to pass a subpath to extract the kraken2 DB

[harmonbhasin]

Due to new updates in permissions made by the krakenDB hosts, the kraken DB can no longer be pulled by passing in the s3 path to nextflow as they've changed permissions on the repo to only allow for unsigned requests (this is an issue as we need to be logged in for aws batch to store files in our private s3 buckets). Currently, Will has downloaded the kraken db to an NAO s3 bucket, however it's large (~70 GB), so we probably don't want to keep downloading this and keeping it.

A better solution would be to pull the KrakenDB during the index workflow by only passing in the subpath, then creating a process that downloads the krakenDB by calling aws s3 cp --no-sign-request followed by the path.

[harmonbhasin]

Turns out if you use "https://" instead of "s3://" it works perfectly fine.