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Fix tests #648

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Merged
merged 5 commits into from
Nov 22, 2024
Merged

Fix tests #648

merged 5 commits into from
Nov 22, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Nov 21, 2024 •
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PR checklist

Tests were failing at mosdepth, and in later stages of annotation. This PR addresses that.

  • 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 Nov 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 74d88aa

+| ✅ 201 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ 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 3.0.2
  • Run at 2024-11-22 08:28:46

@ramprasadn ramprasadn marked this pull request as ready for review November 21, 2024 16:22
fellen31
fellen31 approved these changes Nov 21, 2024
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@fellen31 fellen31 left a comment

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Saw coderabbitai had some suggestions on the mosdepth bioconda recipe PR, did you try those? Otherwise I can take a stab at it at some point.

@ramprasadn
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ramprasadn commented Nov 21, 2024

No, I haven't had the time to implement those changes. But feel free to take a stab at that PR 😄

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fellen31 commented Nov 21, 2024

Could you also mention the removal of d4 in the changelog?

@ramprasadn ramprasadn merged commit e615a7e into dev Nov 22, 2024
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@ramprasadn ramprasadn deleted the update_configs branch January 7, 2025 15:25
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@ramprasadn @fellen31