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Extra columns fix#130

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kbestak merged 5 commits intonf-core:devfrom
kbestak:extra_columns_fix
Nov 18, 2025
Merged

Extra columns fix#130
kbestak merged 5 commits intonf-core:devfrom
kbestak:extra_columns_fix

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@kbestak kbestak commented Nov 17, 2025

I've added that SPOT2CELL and MOLKARTQC can accept inputs with additional columns, as long as the first four are still x, y, z, gene (still without header and tab-separated). This was done to account for optional columns in newly created Molecular Cartography data. Skipping Mindagap with such a table was causing the pipeline to not be usable. Added the appropriate test.

Fixes: #122

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/molkart 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).

@kbestak kbestak linked an issue Nov 17, 2025 that may be closed by this pull request
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LGTM

@kbestak kbestak merged commit 101df3c into nf-core:dev Nov 18, 2025
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@kbestak kbestak deleted the extra_columns_fix branch November 18, 2025 08:43
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Ensure stable outputs if Mindagap is skipped

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