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Use project name in echtvar encode #312

Merged
merged 2 commits into from
Aug 13, 2024
Merged

Use project name in echtvar encode #312

merged 2 commits into from
Aug 13, 2024

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fellen31
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This closes #311, which is a part of #201.

The rest of #201 could be done after adding the module to nf-core, because I think we would need an additional process to generate the json if moving it out of the process..

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,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 Aug 13, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 4007290

+| ✅ 160 tests passed       |+
#| ❔  17 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.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: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-13 17:29:16

@fellen31 fellen31 marked this pull request as ready for review August 13, 2024 10:37
@fellen31 fellen31 requested a review from a team as a code owner August 13, 2024 10:37
@fellen31 fellen31 merged commit ed66340 into genomic-medicine-sweden:dev Aug 13, 2024
14 checks passed
@fellen31 fellen31 deleted the refactor-echtar branch August 13, 2024 18:27
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@jemten jemten jemten approved these changes

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Change echtvar encode COHORT_AF to ${project}_af
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