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Oncoanalyser / Sash stack and glue services #610

Merged
merged 11 commits into from
Oct 27, 2024
Merged

Oncoanalyser / Sash stack and glue services #610

merged 11 commits into from
Oct 27, 2024

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alexiswl
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@alexiswl alexiswl commented Oct 22, 2024 •
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~~ Tests currently failing due to cdk-nag on AWS Step Functions~~

TODO

  • Apply Add nextflow access to data-bucket infrastructure#485 to development account
  • Test oncoanalyser SFN both successfully submitting job and retrieving batch events (and then spitting them out again as workflow run statechange events)
  • Test sash SFN both successfully submitting job and retrieving batch events (and then spitting them out again as workflow run statechange events)

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@alexiswl alexiswl added feature New feature epic labels Oct 22, 2024
@alexiswl alexiswl self-assigned this Oct 22, 2024
@victorskl
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Related umccr/nextflow-stack#115

@reisingerf
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Yup, happy to suppress cdk-nag.

@alexiswl alexiswl marked this pull request as ready for review October 23, 2024 02:31
Alexis Lucattini added 2 commits October 23, 2024 14:28
Remove unused ssm library
b0388fd
Fixes for nf pipeline
07a114c 
* Updated stacky names from mock to stacky
* ICAV2_ACCESS_TOKEN_SECRET_ID an optional env var for fill placeholders lambda
* Add tagResource policy to nf stack
* Fix launch nextflow pipeline sfn
* Fix rule for default Batch event
* Fix batch parameter path link lambda
* Fix override resource requirements
* Add portal run id to engine parameters and to batch parameters
* Add orcabus: true to parameters to allow v1 portal to filter out events
* Fix url extension function
* Fix rna pipeline list flatten
@alexiswl alexiswl requested a review from scwatts October 25, 2024 01:19
scwatts
scwatts approved these changes Oct 25, 2024
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Thanks for the reviewer request, assuming just for visibility - I don't have much context wrt OrcaBus for these changes!

@victorskl
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🥁

@alexiswl alexiswl merged commit 074ac45 into main Oct 27, 2024
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@alexiswl alexiswl deleted the feature/oncoanalyser-nextflow branch October 27, 2024 08:39
@victorskl victorskl mentioned this pull request Oct 28, 2024
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@scwatts scwatts scwatts approved these changes

@victorskl victorskl victorskl approved these changes

@reisingerf reisingerf reisingerf approved these changes

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@alexiswl @victorskl @reisingerf @scwatts