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58 test variant extractor for svs #60

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merged 9 commits into from
Jul 9, 2024

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kubranarci
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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/variantbenchmarking branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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).

@kubranarci kubranarci linked an issue Jul 4, 2024 that may be closed by this pull request
@kubranarci kubranarci requested a review from nvnieuwk July 5, 2024 13:04
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@nvnieuwk nvnieuwk left a comment

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Some comments although I didn't take a thorough look yet

Comment on lines -41 to -42
"minimum": 0,
"maximum": 1
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You can keep these. they won't be validated if the value has not been given

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I wanted to be safe 🗡️ ahaha

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Don't worry it won't break anything :)

modules/local/variant_extractor/main.nf Show resolved Hide resolved
@kubranarci kubranarci requested a review from nvnieuwk July 8, 2024 09:10
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It LGTM 🥳

@kubranarci kubranarci merged commit 9c90ba4 into dev Jul 9, 2024
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@kubranarci kubranarci deleted the 58-test-variant-extractor-for-svs branch July 9, 2024 08:21
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test variant-extractor for SVs
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