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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 · May be fixed by #7090
Open
Tracked by #5828

Add renovate comments to environment.yml #6504

edmundmiller opened this issue Aug 30, 2024 · 2 comments · May be fixed by #7090
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Renovate Version ...

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edmundmiller commented Aug 30, 2024 •
edited by ewels
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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 edmundmiller mentioned this issue Aug 30, 2024
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@edmundmiller edmundmiller self-assigned this Aug 30, 2024
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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 ewels mentioned this issue Sep 27, 2024
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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.

@edmundmiller edmundmiller linked a pull request Nov 25, 2024 that will close this issue
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Renovate Version Update Automation
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Add Renovate env comment linting nf-core/modules
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@ewels @edmundmiller