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nf-core / modules

Repository to host tool-specific module files for the Nextflow DSL2 community!
https://nf-co.re/modules
MIT License
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Add renovate comments to environment.yml #6504

Open edmundmiller opened 2 months ago

edmundmiller commented 2 months ago

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 commented 2 months ago

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 commented 1 month ago

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.