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Fix channel declaration error in the cadd subworkflow #624

Merged
merged 1 commit into from
Oct 4, 2024
Merged

Fix channel declaration error in the cadd subworkflow #624

merged 1 commit into from
Oct 4, 2024

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ramprasadn
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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/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 Oct 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f26c00

+| ✅ 187 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 2024-10-04 08:07:00

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github-actions bot commented Oct 4, 2024

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f26c00

+| ✅ 187 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 2024-10-04 08:07:00

fellen31
fellen31 approved these changes Oct 4, 2024
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@fellen31 fellen31 left a comment

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👍

All tests are stub only right? Could you also "run" CADD then with just a mock path?

@ramprasadn ramprasadn marked this pull request as ready for review October 4, 2024 08:25
@ramprasadn
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Thanks for the review @fellen31. IIRC, the reason we don’t run CADD is that we encounter storage issues on GitHub actions. This is one such workflow that rarely changes so its off by default. Planniing to implement subworkflow level tests soon so that should help.

@ramprasadn ramprasadn merged commit f49a3bb into dev Oct 4, 2024
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@ramprasadn ramprasadn deleted the fix-cadd branch October 31, 2024 22:34
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@ramprasadn @fellen31