[CI] Update CI to include standalone wfs and other wfs

[kapsakcj]

🆒

📌 Explain the Request

Would be good to add CI functionality to test the many standalone workflows so that bugs are caught prior to releases. Workflows like

• ncbi_scrub_PE and SE
• ncbi_amrfinderplus
• sra_fetch
• basespace_fetch
• various Freyja workflows (plot, dashboard, FASTQ, update)
• pangolin_update
• vadr_update (very lower priority, I don't know if anyone even uses this one)
• and many more

We will definitely need to prioritize which workflows that would benefit from this.

Adding these to do a simple miniwdl check in the CI would be a good first step. From there we can get more advanced and thorough and actually run the workflows with miniwdl and cromwell, test for existence of outputfiles, check hashes of those output files, etc., etc.