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Add consensus #145

Merged
merged 6 commits into from
Sep 16, 2024
Merged

Add consensus #145

merged 6 commits into from
Sep 16, 2024

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luisas
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@luisas luisas commented Sep 4, 2024

Add computation of consensus for MSA

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/multiplesequencealign 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>).
  • 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 Sep 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0a17722

+| ✅ 194 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ 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 README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-16 08:59:06

itrujnara
itrujnara approved these changes Sep 4, 2024
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The code is fine, some cosmetic comments added

conf/modules.config Outdated Show resolved Hide resolved
docs/images/nf-core-msa_metro_map.png Outdated
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Full support for dark mode, the logo disappeared somewhere though

nextflow_schema.json Outdated Show resolved Hide resolved
@luisas luisas mentioned this pull request Sep 16, 2024
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@luisas luisas merged commit da8af09 into nf-core:dev Sep 16, 2024
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@luisas luisas deleted the add_consensus branch September 16, 2024 09:10
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@itrujnara itrujnara itrujnara approved these changes

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@luisas @itrujnara