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Add renovate comments to environment.yml #6504

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Tracked by #5828
edmundmiller opened this issue Aug 30, 2024 · 2 comments
Open
Tracked by #5828

Add renovate comments to environment.yml #6504

edmundmiller opened this issue Aug 30, 2024 · 2 comments
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@edmundmiller
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edmundmiller commented Aug 30, 2024

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 #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
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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.

@ewels
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ewels commented Sep 27, 2024

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

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