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Reorder SNV annotation subworkflow to improve performance #585

Merged
merged 5 commits into from
Aug 6, 2024
Merged

Reorder SNV annotation subworkflow to improve performance #585

merged 5 commits into from
Aug 6, 2024

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

Posted for pipeline commit 8c452ff

+| ✅ 186 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 2024-08-06 11:54:45

@ramprasadn ramprasadn marked this pull request as ready for review August 2, 2024 14:31
@ramprasadn ramprasadn requested review from jemten and rannick August 2, 2024 14:31
rannick
rannick reviewed Aug 6, 2024
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subworkflows/local/annotate_genome_snvs.nf Outdated
ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions.first())
ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions.first())
ch_versions = ch_versions.mix(TABIX_VEP.out.versions.first())
ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions)
ch_versions = ch_versions.mix(TABIX_BCFTOOLS_CONCAT.out.versions)
ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions)
//ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions)
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rannick
rannick approved these changes Aug 6, 2024
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LGTM, just a small forgotten comment

@ramprasadn ramprasadn merged commit 511fd3f into dev Aug 6, 2024
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@ramprasadn ramprasadn deleted the vcfanno-split branch August 15, 2024 09:19
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@rannick rannick rannick approved these changes

@jemten jemten Awaiting requested review from jemten

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@ramprasadn @rannick