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Add sex check #453

Merged
merged 5 commits into from
Dec 18, 2023
Merged

Add sex check #453

merged 5 commits into from
Dec 18, 2023

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Lucpen
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@Lucpen Lucpen commented Dec 13, 2023

PR checklist

  • Added sex check from bam file ngsbits sample gender
  • 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).

@Lucpen Lucpen added the WIP Work in progress label Dec 13, 2023
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@Lucpen Lucpen closed this Dec 13, 2023
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github-actions bot commented Dec 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 556e26f

+| ✅ 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 2023-12-18 11:08:30

@Lucpen Lucpen reopened this Dec 13, 2023
@Lucpen Lucpen closed this Dec 13, 2023
@Lucpen Lucpen reopened this Dec 13, 2023
@Lucpen Lucpen changed the base branch from master to dev December 13, 2023 23:18
@Lucpen Lucpen added ready for review PR is ready for review and removed WIP Work in progress labels Dec 15, 2023
@Lucpen Lucpen requested a review from jemten December 15, 2023 13:48
Lucpen
Lucpen commented Dec 18, 2023
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jemten
jemten reviewed Dec 18, 2023
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Nice work! A couple of small comments and suggestions. Let me know what you think of parameterising the ngbits method, we could leave it as is for now.

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@Lucpen Lucpen requested a review from jemten December 18, 2023 11:14
jemten
jemten approved these changes Dec 18, 2023
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Looks good!

@Lucpen Lucpen merged commit b366e66 into nf-core:dev Dec 18, 2023
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@Lucpen Lucpen deleted the add_sex_check branch December 18, 2023 12:06
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@jemten jemten jemten approved these changes

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