Fix conda for upcoming release 2.16.0

[d4straub]

This is fixing conda CI tests.

At first this was intentionally to master branch to run conda CI tests.

Changes include minimum nextflow version 25.04.0 to 25.04.8, an additional package for the DADA2 1.34.0 conda env, change from channel-priority: strict to flexible for CI tests. The latter possibly could be avoided by adding channels to the QIIME2 conda yml file (but that are >700 entries and subject to be update soon anyway, so postponed for now).

PR checklist

• 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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @d4straub,

It looks like this pull-request is has been made against the d4straub/ampliseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the d4straub/ampliseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[d4straub]

So got a few more problems:
(A) conda tests 1,2,3,10,11,13,14

    > Caused by:
    >   Failed to create Conda environment
    >     command: conda env create --prefix /home/runner/_work/ampliseq/ampliseq/~/tests/2207f46f67c288b1a1b8b25489088cf6/work/conda/env-d21b4d68f6431069-86712a09d9a2dd6691411d1f43ad3c03 --file /home/runner/_work/ampliseq/ampliseq/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml
    >     status : 1
    >     message:
    >       CI detected...
    >       2 channel Terms of Service accepted
    >       Channels:
    >        - https://packages.qiime2.org/qiime2/2024.10/amplicon/released
    >        - conda-forge
    >        - bioconda
    >        - defaults
    >       Platform: linux-64
    >       Collecting package metadata (repodata.json): - ��\ ��| ��/ ��- ��\ ��| ��/ ��- ��\ ��| ��/ ��- ��\ ��| ��/ ��- ��\ ��| ��/ ��done
    >       Solving environment: \ ��| ��failed
    >       
    >       LibMambaUnsatisfiableError: Encountered problems while solving:
    >         - package deblur-1.1.1-pyhdfd78af_0 requires sortmerna 2.0, but none of the providers can be installed
    >       
    >       Could not solve for environment specs
    >       The following package could not be installed
    >       └─ deblur =1.1.1 * is not installable because it requires
    >          └─ sortmerna ==2.0 *, which conflicts with any installable versions previously reported.

(B) 6:

     > Caused by:
    >   Failed to create Conda environment
    >     command: conda create --yes --quiet --prefix /home/runner/_work/ampliseq/ampliseq/~/tests/c553c01c2acd08e717490c2fadf9afe7/work/conda/env-93b945977a2cabb4e8a489f140c8d606 -c conda-forge -c bioconda bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2
    [...]
    >       ('Connection broken: IncompleteRead(42946240 bytes read, 37363515 more expected)', IncompleteRead(42946240 bytes read, 37363515 more expected))
    >       ('Connection broken: IncompleteRead(42946240 bytes read, 37363515 more expected)', IncompleteRead(42946240 bytes read, 37363515 more expected))

(C) 7:

     > Caused by:
    >   Failed to create Conda environment
    >     command: conda env create --prefix /home/runner/_work/ampliseq/ampliseq/~/tests/634b12ed63faabe2fe32b8f06dd9e026/work/conda/env-2f4159d5ce53cbd1-c4e426aad9e3430a4b0f8228364b870c --file /home/runner/_work/ampliseq/ampliseq/modules/local/envs/pipesidle-0-1-0-beta.yml
    >     status : 143

Edit: after a re-run of the failed tests (B) turns to (A) and (C) to to a problem with the new DADA2 env
Edit2: I cannot reproduce those errors locally!
Edit3: I can reproduce the error (A) with

conda config --set channel_priority strict
mamba env create -n qiime2-amplicon-2024.10-py310-linux-conda --file ampliseq/modules/local/envs/qiime2-amplicon-2024.10-py310-linux-conda.yml

[ebete]

I think this can be set to strict if the QIIME2 environment definition includes the channel for each package (e.g., bioconda::blast==2.17.0)

[d4straub]

Thanks! But the QIIME2 conda yml file contains 756 lines, and none of the packages are defined with channels, it comes from the QIIME2 developers with that flaw. I would like to keep it as is for now.

[d4straub]

Thanks!