When runnning Conda nf-tests while running CI in my pipeline, I was running into an issue where defaults was being explicitly included as a channel in the conda configuration, leading to warnings and errors in some Conda processes:

    > WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    >     There is a problem with your Conda configuration!
    >     You will need to set-up the conda-forge and bioconda channels correctly.
    >     Please refer to https://bioconda.github.io/
    >     The observed channel order is
    >     [defaults]
    >     but the following channel order is required:
    >     [conda-forge, bioconda]
    > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"

The CI setup showed that the condrc files looked like the following, with no channels set up for the runner user after defaults removal:

  ==> /usr/share/miniconda/.condarc <==
  channels:
    - defaults
 
  ==> /home/runner/.condarc <==
  auto_update_conda: True
  auto_activate: True
  notify_outdated_conda: False
  changeps1: False
  pkgs_dirs:
    - /home/runner/conda_pkgs_dir
  channels: []
  always_yes: True
  solver: libmamba

This PR explicitly sets channels in the conda setup so that we don't get this problem of falling back onto the system condarc file.

There's also an option in the setup-miniconda action to explicitly install miniforge, which shouldn't ever have defaults configured in the first place. Might be an alternative to this approach?

https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#example-10-miniforge

See https://nfcore.slack.com/archives/C04QR0T3G3H/p1758020637890609 for discussion

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
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• Documentation in docs is updated