TEMPLATE: Add bioconda channel to conda setup

[maxulysse]

cf

nf-core/sarek#2106

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[mashehu]

I think that should be specified in the environment.yml files not here or what was the problem?

[maxulysse]

when launching a pipeline in the CI in conda, we had the warning that the conda channels were not set up properly due to
https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/utils_nextflow_pipeline/main.nf#L107

[maxulysse]

it's a pipeline level conda configuration issue in my opinion, so I'd say that's the right place for the fix

[maxulysse]

@mashehu and I talked, and we agreed that there is some more to it than just that, and the whole conda check function might need an overall.

To recapitulate for everyone.
Because I went a bit overboard with the testing in sarek thanks to nft-utils, I now capture for the default test the full terminal output, and catch all WARNING messages.
That led to the discovery on the current sarek release that the conda channels were not properly setup.
I assume this warning is on every pipeline but no-one noticed it because no one reads the logs when the pipeline is not failing.
This whole check failure is, we think, misleading, because we set up the conda channels in the conda profile at the nextflow level, but the check is done by executing conda itself.
So the conda check function should be done by checking the channels available within nextflow (I assume in the conda scope).
And that should be parameterized as some pipeline do not need bioconda.

I leave the decision of merging this in TEMPLATE to @mashehu