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added tests folder and updates fitness_calculation.R#33

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MaximilianStammnitz merged 1 commit intodevfrom
fix-fitness-and-tests
Mar 6, 2026
Merged

added tests folder and updates fitness_calculation.R#33
MaximilianStammnitz merged 1 commit intodevfrom
fix-fitness-and-tests

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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/deepmutscan 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).

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@BenjaminWehnert1008 please remove the new '\' signs from the fitness_calculation.R file; these would mess with the run

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BenjaminWehnert1008 commented Mar 6, 2026

For me, locally, it doesn't work without. I think it's because it tries to interpret everything after $ as a Nextflow parameter


Caused by:
  Failed to parse template script (your template may contain an error or be trying to use expressions not currently supported): org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  /groovy/script/ScriptFEA89ADE780AB746C2B7FA537C9A6C4A: 72: token recognition error at: ''' @ line 72, column 21.
           merged.counts$'wt_aa'[i] <- tmp.wt[merged.counts$pos[i]]

@MaximilianStammnitz MaximilianStammnitz merged commit 8b15bec into dev Mar 6, 2026
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@MaximilianStammnitz MaximilianStammnitz deleted the fix-fitness-and-tests branch March 6, 2026 14:43
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2 participants