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Subworkflow for mobile element annotation #483

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Merged
merged 7 commits into from
Jan 19, 2024
Merged

Subworkflow for mobile element annotation #483

merged 7 commits into from
Jan 19, 2024

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jemten
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@jemten jemten commented Jan 18, 2024 •
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This PR adds the option to annotate the mobile elements with SVDB and VEP

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>).
  • 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 Jan 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d14976b

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-19 10:29:46

@jemten jemten marked this pull request as ready for review January 18, 2024 13:44
@jemten jemten requested a review from ramprasadn January 19, 2024 09:55
Lucpen
Lucpen reviewed Jan 19, 2024
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Only very very minor comments :)

@jemten @Lucpen
Apply suggestions from code review
d14976b 
Co-authored-by: Lucía Peña-Pérez <lucia.pena.perez@scilifelab.se>
Lucpen
Lucpen approved these changes Jan 19, 2024
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LGTM!

@jemten jemten merged commit d36de29 into nf-core:dev Jan 19, 2024
@jemten jemten deleted the me_anno branch January 19, 2024 14:04
This was referenced Jan 19, 2024
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@Lucpen Lucpen Lucpen approved these changes

@ramprasadn ramprasadn Awaiting requested review from ramprasadn

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@jemten @Lucpen
点击 这是indexloc提供的php浏览器服务，不要输入任何密码和下载