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Re-factor code for ivar_variants_to_vcf script #304

Merged
merged 12 commits into from
Apr 14, 2022
Merged

Re-factor code for ivar_variants_to_vcf script #304

merged 12 commits into from
Apr 14, 2022

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saramonzon
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@saramonzon saramonzon commented Apr 13, 2022 •
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As we've talked here #258 , here it is a proposal for ivar_variants_to_vcf script, hope this helps understanding and maintaining the script. In any case now it would be pretty easier to split it in two scripts if needed.

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/viralrecon 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>).
  • 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).

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github-actions bot commented Apr 13, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 62d3302

+| ✅ 138 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowViralrecon.groovy

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-04-14 10:29:14

@drpatelh
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Can we add an entry to the CHANGELOG please?

drpatelh
drpatelh approved these changes Apr 14, 2022
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@drpatelh drpatelh merged commit 7c787e0 into nf-core:dev Apr 14, 2022
@saramonzon saramonzon changed the title Re-factor code (proposal) for ivar_variants_to_vcf script Re-factor code for ivar_variants_to_vcf script Apr 26, 2022
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@drpatelh drpatelh drpatelh approved these changes

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@saramonzon @drpatelh