[ORCA-297] Fixing tutorial demo (demo.py and documentation)

[jaymedina]

problem

The initial problem was the demo.py was failing at step: monitor_synstage due to it still pointing at the old nf-synstage workflow which runs with DSL1 which is no longer supported:

Further blockers involved failures at step monitor_rnaseq. More context in solution below.

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solution

• Point demo.py to the new synstage.nf workflow in the nf-synapse repository.
• Fix S3 AccessDenied error by changing s3_prefix in example to a bucket that DPE tower/tower-dev workspaces have access to, and adding a caveat that the s3_prefix should be accessible by the tower workspace you're launching from.
• Mention in documentation that NF_SYNSTAGE workflow runs should have unique names (i.e. no consecutive runs of my_test_dataset_synstage with a _# tacked on at the end). Otherwise, this will lead to consecutive steps breaking because the samplesheet can't be found.
• Co-authored with @BWMac : Fix incorrect directory path in get_staged_samplesheet
• Update documentation in README.md and demo.py

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testing & preview

With the changes noted above, all steps up until monitor_synindex pass, which is expected behavior ✅ :

source

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out of scope

It has been discovered that the current demo.py is not written to support getting staged samplesheets from consecutive runs of synstage with the same run name, due to the way the names are updated (e.g. my_test_dataset_synstage_2, my_test_dataset_synstage_3, etc.

This is out of scope but is a nice-to-have, low priority item that can be moved to the bottom of the backlog. In the meantime, documentation will be updated in this PR to notify users that runs of NF_SYNSTAGE should have unique names.

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This is a blocker for IBCDPE-749 and therefore high in urgency 🔥

[swarmia]

✅  Linked to Story ORCA-297 · Update py-orca's demo.py

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (433e7ae) 100.00% compared to head (0517118) 100.00%.

Additional details and impacted files

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  Coverage   100.00%   100.00%           
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  Files           28        28           
  Lines          920       920           
  Branches       140       140           
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  Hits           920       920           

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[thomasyu888]

🔥 Nice!

[sonarcloud]

Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[thomasyu888]

🔥 this is great! If my memory serves me right, the synindex steps fails right now - eventually we will make it all work!