Remove balsamic r flag

[seallard]

Description

This PR replaces the -r --run-analysis with the dry run flag. Closes #2722.

The -r flag ensured that slurm jobs only were run for balsamic with the --run-analysis option if it was provided to the cli initiating the balsamic run. It seems like this is no longer desired, the dry run flag now replaces this behavior. So the --run-analysis will not be used for the balsamic run if dry run is provided.

Fixed

• Replace the -r flag with just the dry run flag for balsamic

This version is a

• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[fevac]

❤️ yes, this looks like what we want to me. Note that merging this has to be sync with cron/systemd

[ivadym]

Nice ⚡ 💯 Left you a tiny comment so we have the same expected behaviour with the dry-run as before

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
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0.0% Duplication

[ivadym]

Tests look fine in Stage 🥳 👍

We need to update automation and atlas documentation. I will do the latter in this PR: https://github.com/Clinical-Genomics/atlas/pull/2167

[seallard]

Tests look fine in Stage 🥳 👍

We need to update automation and atlas documentation. I will do the latter in this PR: Clinical-Genomics/atlas#2167

I checked the servers repo and from what I can see we only use the start available cli command to queue balsamic jobs (which does not use the --run-analysis flag). So I do not think any update is necessary. Unless I've missed something @ivadym

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[ivadym]

Yes, you're right we had the run_analysis flag set to True in start available, so the logic was in CG 👍