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changed valid values for the sex variable #550

Merged
merged 5 commits into from
May 20, 2024
Merged

changed valid values for the sex variable #550

merged 5 commits into from
May 20, 2024

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sima-r
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@sima-r sima-r commented May 16, 2024 •
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This is now compatible with the PED file format and the documentation.

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).

@sima-r
changed valid values for sex
03b0e9d 
This is now compatible with the PED file format and documentation
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github-actions bot commented May 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8b380e3

+| ✅ 183 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 2024-05-20 09:33:50

@sima-r sima-r mentioned this pull request May 16, 2024
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sima-r commented May 16, 2024 •
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@ramprasadn I wasn't sure about the base branch for this PR. Just let me know if this patch branch is not the best choice,
And I couldn't figure out the linting errors 😬 plz teach me what the problem is so I know it next time, lol

@sima-r sima-r linked an issue May 16, 2024 that may be closed by this pull request
Error when 'other' is given as gender #549
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@sima-r sima-r requested a review from ramprasadn May 16, 2024 08:47
@sima-r sima-r self-assigned this May 16, 2024
@sima-r sima-r requested a review from jemten May 16, 2024 08:49
@ramprasadn ramprasadn changed the base branch from patch to dev May 18, 2024 12:54
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ramprasadn commented May 18, 2024 •
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Hi @sima-r! I have changed the base from patch to dev since these changes will be going into a minor release. As for the lint error, it was related changes in the recent template merge. It has been addressed in the dev branch so a merge with the current dev should fix it (specifically, I added this line to fix this error).

raredisease/.nf-core.yml

Line 10 in ae1d495

modules_config: False

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ramprasadn requested changes May 18, 2024
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@sima-r Could you update the CHANGELOG.md file?

@sima-r sima-r requested a review from ramprasadn May 20, 2024 09:30
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Thanks @sima-r !

@sima-r sima-r merged commit 4a9bb55 into dev May 20, 2024
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@sima-r sima-r deleted the inputschemafixes branch May 20, 2024 09:45
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@ramprasadn ramprasadn ramprasadn approved these changes

@jemten jemten Awaiting requested review from jemten

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Error when 'other' is given as gender
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