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Apply review corrections and tool version update #265

Merged
merged 11 commits into from
Jun 5, 2023
Merged

Apply review corrections and tool version update #265

merged 11 commits into from
Jun 5, 2023

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ggabernet
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  • clean up unnecessary quotes
  • fix quote
  • remove quay.io from containers
  • update to Enchantr 0.1.2
  • update nf-core modules
  • apply review comments
  • apply review comments

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/airrflow 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>).
  • 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).

@ggabernet ggabernet marked this pull request as ready for review June 5, 2023 13:29
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github-actions bot commented Jun 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 68ddf0a

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.1.0'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-05 13:39:12

@ggabernet ggabernet mentioned this pull request Jun 5, 2023
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@ggabernet
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@nf-core-bot fix linting

@ggabernet ggabernet requested a review from ssnn-airr June 5, 2023 13:57
@ggabernet ggabernet merged commit f235c82 into nf-core:dev Jun 5, 2023
@ggabernet ggabernet deleted the enchantr-update branch June 22, 2023 17:55
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Reviewers

@ssnn-airr ssnn-airr ssnn-airr approved these changes

@adamrtalbot adamrtalbot Awaiting requested review from adamrtalbot

@maxulysse maxulysse Awaiting requested review from maxulysse

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@ggabernet @ssnn-airr @nf-core-bot