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First pipeline release#54

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BenjaminWehnert1008 wants to merge 500 commits into
masterfrom
dev
Open

First pipeline release#54
BenjaminWehnert1008 wants to merge 500 commits into
masterfrom
dev

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@BenjaminWehnert1008

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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/dmscore branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

BenjaminWehnert1008 and others added 30 commits August 28, 2025 17:55
Renamed README descriptions from nf-core/dmscore to nf-core/deepmutscan
Added note on the importance of including wildtype synonymous codons in the original mutagenesis design.
removing underscores in sample name merges (DiMSum experimental design sheet)
@BenjaminWehnert1008

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@mashehu, how does it come that some tests are failing now, if all checks have been successfull before pulling to the master?
Especially, I'm wondering about a new linting error. There also seems to be an issue creating a conda env.
Are those typical pitfalls when pulling from the dev branch? Thanks!

@mashehu

mashehu commented Jun 15, 2026

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PRs against master/main get linted with --release that has some additional rules. we also run nf-test with conda and singularity, which is usually left out in dev. looks like you need to specify an additional dependency in the environment.yml of your tool

@BenjaminWehnert1008 BenjaminWehnert1008 requested review from mashehu and removed request for mashehu June 23, 2026 10:47
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4 participants