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Refactor reference channels #443

Merged
merged 3 commits into from
Oct 30, 2024
Merged

Refactor reference channels #443

merged 3 commits into from
Oct 30, 2024

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fellen31
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@fellen31 fellen31 commented Oct 29, 2024 •
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This PR tries to standardise creation of inputs reference channels, and also moves validation of the vep plugin files to nf-schema, via samplesheetToList.

Should wait for nf-schema 2.2.0 to be added to the nextflow plugins repository:

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 refactor-inputs branch 5 times, most recently from 036da2c to c333d53 Compare October 30, 2024 10:44
@fellen31 fellen31 marked this pull request as ready for review October 30, 2024 10:53
@fellen31 fellen31 requested a review from a team as a code owner October 30, 2024 10:53
peterpru
peterpru approved these changes Oct 30, 2024
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Looks good to me!

@fellen31 fellen31 merged commit 0b2b81c into genomic-medicine-sweden:dev Oct 30, 2024
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@fellen31 fellen31 deleted the refactor-inputs branch October 30, 2024 16:32
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@peterpru peterpru peterpru approved these changes

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