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Add renovate comments to environment.yml

Open edmundmiller opened this issue 1 year ago • 2 comments

Essentially we need to add to all the environment.ymls

channels:
  - conda-forge
  - bioconda
dependencies:
  # renovate: datasource=conda depName=bioconda/bwa
  - bwa=0.7.18
  # renovate: datasource=conda depName=bioconda/samtools
  - samtools=1.20
  # renovate: datasource=conda depName=bioconda/htslib
  - htslib=1.20.0

We can also keep the channel definitions if the consensus is that they're important. I've got a PR to enable either https://github.com/nf-core/modules/pull/5400

channels:
  - conda-forge
  - bioconda
dependencies:
  # renovate: datasource=conda depName=bioconda/bwa
  - bioconda::bwa=0.7.18
  # renovate: datasource=conda depName=bioconda/samtools
  - bioconda::samtools=1.20
  # renovate: datasource=conda depName=bioconda/htslib
  - bioconda::htslib=1.20.0

edmundmiller avatar Aug 30 '24 12:08 edmundmiller

Discussed in the maintainers meeting. Keeping the bioconda:: because we can, and that way we're specific about it. We'll support the dependencies without the channel as well.

edmundmiller avatar Aug 30 '24 13:08 edmundmiller

Related: https://github.com/nf-core/tools/issues/3184 for tools integration. If that's done first, the bulk addition in this PR can be automated.

ewels avatar Sep 27 '24 22:09 ewels