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5% frequency threshold for mitochondrial clinical vcfs #616

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Merged
merged 6 commits into from
Sep 25, 2024
Merged

5% frequency threshold for mitochondrial clinical vcfs #616

merged 6 commits into from
Sep 25, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Sep 24, 2024

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

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github-actions bot commented Sep 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 931fc00

+| ✅ 187 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 2024-09-24 16:31:52

@ramprasadn ramprasadn requested a review from jemten September 24, 2024 13:39
@ramprasadn ramprasadn marked this pull request as ready for review September 24, 2024 13:59
@ramprasadn ramprasadn requested a review from Lucpen September 24, 2024 13:59
jemten
jemten approved these changes Sep 24, 2024
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LGTM

jemten
jemten reviewed Sep 24, 2024
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conf/modules/generate_clinical_set.config
withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_FILTER' {
ext.when = !params.skip_vep_filter
ext.prefix = { "${meta.id}_mt_${meta.set}" }
ext.args = { "-Oz -i 'AF>0.05'" }
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@jemten jemten Sep 24, 2024

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Could be good to add a line in the documentation saying that the default is not to output variants with a VAF below 5%.

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@ramprasadn ramprasadn Sep 24, 2024

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Done! 👍🏻

@ramprasadn ramprasadn merged commit df4db70 into dev Sep 25, 2024
@ramprasadn ramprasadn deleted the bcftools-filter branch October 1, 2024 14:19
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@jemten jemten jemten approved these changes

@Lucpen Lucpen Awaiting requested review from Lucpen

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@ramprasadn @jemten