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Fix miniconda version - #12879

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LouisLeNezet:miniconda_version
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Fix miniconda version#12879
LouisLeNezet wants to merge 1 commit into
nf-core:masterfrom
LouisLeNezet:miniconda_version

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@LouisLeNezet

@LouisLeNezet LouisLeNezet commented Sep 3, 2026

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PR checklist

This PR fix the miniconda_version used in nf-test action.
The issue arose with phyloflash module with the following error for conda test:
https://github.com/nf-core/modules/actions/runs/31088940040/job/92575211202

Installing package 'bioconda::spades-3.15.5-h95f258a_1'
...
LinkError: post-link script failed
.../.spades-post-link.sh
...
deactivate-gxx_linux-64.sh: line 68:
CONDA_BACKUP_CXX: unbound variable

This seems to be linked to
conda/conda#9966

But i couldn't manage to fix it with set +eu flags.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@LouisLeNezet
LouisLeNezet requested review from a team as code owners September 3, 2026 14:04
@LouisLeNezet
LouisLeNezet requested review from mahesh-panchal and removed request for a team September 3, 2026 14:08

@mahesh-panchal mahesh-panchal left a comment

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My only comment is that we need something to make sure this version doesn't go stale when/if it gets fixed.

@LouisLeNezet

LouisLeNezet commented Sep 3, 2026

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My only comment is that we need something to make sure this version doesn't go stale when/if it gets fixed.

I don't really see a solution for that, as conda release each month a new version.
I guess this issue might stay open for quite a time, or should I open an issue on conda github account to follow it ?

@mahesh-panchal

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I would say you subscribe to the issue on there so you get any notifications of changes. Make an issue here that describes what needs to be done when that issue is closed. Then merge this in.

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2 participants