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Filter SNVs, INDELs, CNVs and SVs #496

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merged 12 commits into from
Nov 19, 2024

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@fellen31 fellen31 commented Nov 7, 2024

Closes #329, calls it filtered instead of clinical_set to be a bit more general.

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
  • 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).

@fellen31 fellen31 force-pushed the filter-variants branch 2 times, most recently from 03c1388 to 7e2223b Compare November 7, 2024 15:17
@fellen31 fellen31 changed the title Filter variants Filter SNVs, INDELs, CNVs and SVs Nov 7, 2024
@fellen31 fellen31 marked this pull request as ready for review November 7, 2024 15:31
@fellen31 fellen31 requested a review from a team as a code owner November 7, 2024 15:31
@fellen31 fellen31 marked this pull request as draft November 7, 2024 15:32
@fellen31 fellen31 marked this pull request as ready for review November 7, 2024 15:35
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@Schmytzi Schmytzi left a comment

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Good work but some things that should be adressed (mostly related to gawk)

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@fellen31 fellen31 force-pushed the filter-variants branch 2 times, most recently from 1086988 to 9c9020e Compare November 12, 2024 17:37
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  • Removed the HGNC: part in nallo.nf.
  • Removed # from the header requirements and updated testdata (now hgnc_id).
  • Check for both integer and string types in schema to match both e.g. 4826 and HGNC:4826.

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Nice work! Had a couple of comments.

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👍

@fellen31 fellen31 merged commit e9ff17c into genomic-medicine-sweden:dev Nov 19, 2024
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@fellen31 fellen31 deleted the filter-variants branch November 19, 2024 07:27
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