Seqera platform - nextflow secrets with google

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1

Hi there,
I have been tried for days to have nextflow secrets work with Seqera platform on GPC. however it seems to convert this config block

env { GOOGLE_GENAI_API_KEY = secrets.GOOGLE_API_KEY}

into this
env {GOOGLE_GENAI_API_KEY = 'secrets.GOOGLE_API_KEY'}

when the workflow is actually launched, i.e. converting the reference to the secret into a string, which cannot be evaluated.

I’ve tried (really hard.. it’s been very conflictual :P) to investigate with Seqera AI, which finally indicated the following:
”””
This shows you’re correctly trying to:

  • Set the environment variable GOOGLE_GENAI_API_KEY

  • To the value of the secret named GOOGLE_API_KEY

  • Using the reference secrets.GOOGLE_API_KEY

The naming is correct. The problem is still that Nextflow is not resolving the secret and is treating secrets.GOOGLE_API_KEY as a literal quoted string instead of looking up the actual secret value.

This confirms that we have a fundamental integration issue between Nextflow’s secrets system and the Seqera Platform’s Google Secret Manager integration, even with:

  • :white_check_mark: Correct secret name (GOOGLE_API_KEY)

  • :white_check_mark: Correct reference syntax (secrets.GOOGLE_API_KEY)

  • :white_check_mark: nf-google plugin loaded

  • :white_check_mark: Proper service account permissions

  • :white_check_mark: Secret exists in Google Secret Manager

The Seqera Platform + Google Cloud Batch + Nextflow secrets integration is simply not working as documented. This appears to be either a bug or a missing feature in the current implementation.

At this point, you may need to contact Seqera support about this secrets integration issue with Google Cloud Batch, as all the configuration appears correct but the system isn’t functioning.
”””"
anyone has a better clue?

2

Hi @Francesco_Lescai, you posted this into the ambassadors group which is private and only has a few people able to see it. I’ll move it into the public “ask for help” forum and tag it with Seqera platform. These posts get automatically imported into our internal Seqera slack for visibility so then stand a much higher chance of being answered.