Added new script for running oncoanalyser through orcabus

[alexiswl]

• Use a manifest json as input

• Assumes nextflow roles have permissions to read/write to cache buckets

• Supports both DNA only (from bam), RNA only (from fastq) and DNA + RNA (from post-oncoanalyser) workflows

• Params now stored in params.json

• Use jq to build param args and samplesheet csv

[scwatts]

Thanks so much, and truly next level use of jq!

Have you tested this in dev? If not happy to give it a go

[scwatts]

Were there any further changes needed to switch from subject ID to library ID?

[alexiswl]

Have you tested this in dev? If not happy to give it a go

No not yet, just getting the structure right first, we will need to also manually give the oncoanalyser roles permissions to access the data-account buckets as well before we can start testing

[alexiswl]

Were there any further changes needed to switch from subject ID to library ID?

I don't think so, for now we can just continue to use the SBJ nfrom the linked individual object, this is set via the orchestration rather than the nextflow stack too so we can change this down the track without needing to make changes here

[scwatts]

Great, that makes it easy though I will probably change variable names from subject to library or similar when that time comes

For testing is there anything stopping us from using the current S3 bucket to avoid permissions issues? e.g. manually stage inputs into our temp dev bucket then provide an appropriate manifest to the run-v2.sh script. I'd love to test this early in the dev process if possible

[victorskl]

(subscribed)

[victorskl]

@scwatts We had a discussion/update yesterday in devops. Just want to loop you in.

This PR intertwined with OrcaBus O3 release.

I understood that changes contain in this PR, added extension to OrcaBus automation (and doest not affect to existing ops with Portal automation).

So, we probably need to deploy this to prod after testing has performed (tbc in #arteria-dev and #alerts-dev for events).

FYI