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Merged
merged 2 commits into from
Nov 15, 2023
Merged

Document which variantcatalogs to use #443

merged 2 commits into from
Nov 15, 2023

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jemten
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@jemten jemten commented Nov 14, 2023

As reported in #439, it is not clear that you need to use a special variant catalog for the repeat expansion workflow to work.

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 Nov 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit beb425c

+| ✅ 151 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 2.10
  • Run at 2023-11-15 09:53:22

@jemten jemten linked an issue Nov 14, 2023 that may be closed by this pull request
Document which variant catalogs to use for expansionhunter-stranger #439
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@jemten jemten requested a review from ramprasadn November 14, 2023 13:56
ramprasadn
ramprasadn approved these changes Nov 15, 2023
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LGTM! 🚀

@jemten jemten merged commit cfe371f into dev Nov 15, 2023
@jemten jemten deleted the document_variantca branch November 15, 2023 12:43
@jemten jemten mentioned this pull request Nov 15, 2023
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Document which variant catalogs to use for expansionhunter-stranger

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@jemten @ramprasadn
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