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Fix intervals with dot #1403

Merged
merged 7 commits into from
Feb 14, 2024
Merged

Fix intervals with dot #1403

merged 7 commits into from
Feb 14, 2024

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maxulysse
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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/sarek 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>).
  • 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 Feb 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 16dbe97

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-14 12:59:23

@maxulysse maxulysse mentioned this pull request Feb 13, 2024
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@maxulysse
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so using baseName over simpleName because some species have . (dot` in the chromosome name...

@FriederikeHanssen
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that makes a ton of sense. 🐛

@maxulysse
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that makes a ton of sense. 🐛

I'm impressed it took that long to got to this issue.

FriederikeHanssen
FriederikeHanssen approved these changes Feb 14, 2024
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nice one

@maxulysse maxulysse merged commit 68a1fa7 into nf-core:dev Feb 14, 2024
45 of 59 checks passed
@maxulysse maxulysse deleted the intervals_dot branch February 14, 2024 15:11
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen