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nf-core lint should say which conda packages are not specified correctly #3009

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mahesh-panchal opened this issue May 30, 2024 · 0 comments
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@mahesh-panchal
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Description of feature

When doing nf-core lint,
a line like: conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
can result in multiple Conda version not specified correctly:

│ breadthofcoverage               │ modules/local/breadthofcoverage.nf             │ Conda version not specified correctly                                                   │
│ plotauthenticationscore         │ modules/local/plotauthenticationscore.nf       │ Conda version not specified correctly                                                   │
│ plotauthenticationscore         │ modules/local/plotauthenticationscore.nf       │ Conda version not specified correctly                                                   │
│ plotauthenticationscore         │ modules/local/plotauthenticationscore.nf       │ Conda version not specified correctly                                                   │
│ plotauthenticationscore         │ modules/local/plotauthenticationscore.nf       │ Conda version not specified correctly                                                   │

but this is hard to figure out what is triggering the linting.

ewels added a commit that referenced this issue May 31, 2024
Tried to do this with GitHub Copilot Workspaces but it failed 😅 

As I was looking at the code anyway I could see the fix so figured I would put it manually.

Closes #3009

Untested, done in web browser only.
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