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Bcftools roh logic update #579

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Merged
merged 5 commits into from
Jul 2, 2024
Merged

Bcftools roh logic update #579

merged 5 commits into from
Jul 2, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Jul 2, 2024

PR checklist

This PR introduces a change to skip bcftools roh when there are no affected samples in a case.

  • 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 Jul 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cccad16

+| ✅ 185 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 2024-07-02 12:37:23

@ramprasadn ramprasadn marked this pull request as ready for review July 2, 2024 12:39
@ramprasadn ramprasadn requested a review from jemten July 2, 2024 12:39
jemten
jemten approved these changes Jul 2, 2024
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👍

conf/modules/annotate_genome_snvs.config
process {

withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH' {
ext.when = { meta.probands.size()>0 }
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@jemten jemten Jul 2, 2024

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nice!

@ramprasadn ramprasadn merged commit dd8dd88 into dev Jul 2, 2024
@ramprasadn ramprasadn deleted the bcftools_roh_update branch July 2, 2024 15:25
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten