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Updating tests and documentation to correct 'scaled' distances #16

Merged
merged 3 commits into from
Jun 27, 2024
Merged

Updating tests and documentation to correct 'scaled' distances #16

merged 3 commits into from
Jun 27, 2024

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kylacochrane
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This PR updates the documentation (README), parameter check, and tests related to scaled distances. There was previously a misunderstanding in the permissible range of scaled distance thresholds. We believed these were [0.0, 1.0], but they are actually [0.0, 100.0] (i.e. percentages).

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!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jun 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d2e2c80

+| ✅ 146 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/gasnomenclature/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/nextflow_schema.json

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/gasnomenclature/gasnomenclature/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-26 21:34:40

@kylacochrane kylacochrane marked this pull request as ready for review June 25, 2024 13:01
@kylacochrane kylacochrane requested a review from apetkau June 25, 2024 13:01
apetkau
apetkau requested changes Jun 26, 2024
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This looks great Kyla. I just have one comment, and I'm going to ask for more clarification on this.

apetkau
apetkau reviewed Jun 26, 2024
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Updated with more information based on internal discussion of clustering methods.

apetkau
apetkau approved these changes Jun 27, 2024
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This looks great. Thanks so much Kyla 😄

@kylacochrane kylacochrane merged commit c6d4ba6 into dev Jun 27, 2024
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@kylacochrane kylacochrane deleted the update_scaled branch June 27, 2024 17:38
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@apetkau apetkau apetkau approved these changes

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@kylacochrane @apetkau