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updating meta.sex type check #559

Merged
merged 2 commits into from
May 28, 2024
Merged

updating meta.sex type check #559

merged 2 commits into from
May 28, 2024

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jemten
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@jemten jemten commented May 27, 2024

This PR updates the meta.sex checks

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 May 27, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6ec160f

+| ✅ 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 2024-05-27 14:41:58

@jemten jemten marked this pull request as ready for review May 27, 2024 09:31
@jemten jemten requested a review from ramprasadn May 27, 2024 09:31
ramprasadn
ramprasadn reviewed May 27, 2024
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subworkflows/local/gens.nf Outdated
@@ -36,8 +36,8 @@ workflow GENS {

COLLECTREADCOUNTS.out.hdf5
.branch { meta, counts ->
female: meta.sex.equals(2) || meta.sex.equals(0)
male: meta.sex.equals(1)
female: meta.sex.equals('2') || meta.sex.equals('other')
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Looks fine to me, but have you checked a test case through this to make sure that this works as expected? :)

And perhaps you can use matches instead of equals here?

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I tried enabling the gens subworkflow and ran a stub run and was then able to get collectreadscounts to execute, which it didn't before.

Good point about matches. Will update

ramprasadn
ramprasadn approved these changes May 27, 2024
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LGTM!

@jemten jemten merged commit 94f782d into dev May 28, 2024
6 checks passed
@jemten jemten deleted the fix_gens_sex branch May 28, 2024 06:50
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@ramprasadn ramprasadn ramprasadn approved these changes

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@jemten @ramprasadn