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chromograph autozyg#523

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ramprasadn merged 2 commits into
nf-core:devfrom
genomic-medicine-sweden:autozyg
Feb 29, 2024
Merged

chromograph autozyg#523
ramprasadn merged 2 commits into
nf-core:devfrom
genomic-medicine-sweden:autozyg

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@ramprasadn

@ramprasadn ramprasadn commented Feb 29, 2024

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PR checklist

Addresses Clinical-Genomics#16

  • 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>).
  • 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).

@ramprasadn ramprasadn marked this pull request as ready for review February 29, 2024 08:03
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github-actions Bot commented Feb 29, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e280515

+| ✅ 177 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-29 12:22:39

@ramprasadn ramprasadn requested a review from jemten February 29, 2024 12:16
jemten
jemten approved these changes Feb 29, 2024
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👍

@ramprasadn ramprasadn merged commit 7bf014f into nf-core:dev Feb 29, 2024
@ramprasadn ramprasadn deleted the autozyg branch February 29, 2024 12:39
@jemten jemten mentioned this pull request Mar 1, 2024
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten