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Include "other" variants for CADD to analyse multallelic indels #545

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merged 3 commits into from
May 14, 2024
Merged

Include "other" variants for CADD to analyse multallelic indels #545

merged 3 commits into from
May 14, 2024

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fa2k
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@fa2k fa2k commented May 6, 2024 •
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This PR solves a problem (#544 ), that not all alleles at a multiallelic indel site get a CADD score. The issue is that all indels aren't selected by bcftools view .... --types indels even though they are indels. Only the first indel at a position is selected by bcftools view and therefore scored. The PR includes the "other" variant type in the selection of variants for CADD. It doesn't seem to include a large number of additional variants, so I don't think it will slow down the pipeline significantly.

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!
    (Not possible to test CADD due to the huge database size)
  • 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 lint).
    There are warnings & errors, but they seem unrelated.
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
    CADD is disabled in these tests. I've run a test on a bigger dataset.
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
    Fails in GENMOD, seems unrelated.
  • 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.
    (Will be updated after I get the pull request link)
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented May 6, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9465bc8

+| ✅ 182 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-14 15:13:15

@fa2k fa2k marked this pull request as ready for review May 6, 2024 17:50
@ramprasadn
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Could you sync your changes with the latest dev @fa2k ? Hopefully, that will fix the lint error.

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fa2k commented May 14, 2024 •
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@ramprasadn This seems to have worked :)

ramprasadn
ramprasadn approved these changes May 14, 2024
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LGTM!

@fa2k fa2k merged commit fe5d362 into nf-core:dev May 14, 2024
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@ramprasadn ramprasadn ramprasadn approved these changes

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@fa2k @ramprasadn