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Use distinct output filenames for bcfools and svdb#716

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ramprasadn merged 4 commits into
nf-core:devfrom
alexiandra97:fix_svdb_merge
Oct 9, 2025
Merged

Use distinct output filenames for bcfools and svdb#716
ramprasadn merged 4 commits into
nf-core:devfrom
alexiandra97:fix_svdb_merge

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@alexiandra97

@alexiandra97 alexiandra97 commented Aug 19, 2025

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When running the pipeline, the same filename was used for both the input and output. It's related to #686

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_singleton,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).

@nf-core-bot

nf-core-bot commented Aug 19, 2025

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

jemten
jemten approved these changes Aug 26, 2025
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@jemten jemten left a comment

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Looks good to me

@ramprasadn ramprasadn merged commit 23982d0 into nf-core:dev Oct 9, 2025
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@ramprasadn ramprasadn mentioned this pull request Oct 9, 2025
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@jemten jemten jemten approved these changes

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@alexiandra97 @nf-core-bot @jemten @ramprasadn