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Updating usage.md #1556

Merged
merged 2 commits into from
Jun 10, 2024
Merged

Updating usage.md #1556

merged 2 commits into from
Jun 10, 2024

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asp8200
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@asp8200 asp8200 commented Jun 10, 2024 •
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https://nfcore.slack.com/archives/CE7DN1U7M/p1718026925433339?thread_ts=1718025669.110949&cid=CE7DN1U7M

Those commands in the conf/usage.md now seem to be rendered correctly:

https://github.com/nf-core/sarek/blob/a2ecdcb98c0c28f22ba45f369190614de3e1c473/docs/usage.md#where-do-the-used-reference-genomes-originate-from

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/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test tests/ --verbose --profile +docker).
  • 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).

@asp8200 asp8200 changed the title Adding some ticks around some commands Updating usage.md Jun 10, 2024
maxulysse
maxulysse approved these changes Jun 10, 2024
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looking good already

@asp8200 asp8200 marked this pull request as ready for review June 10, 2024 14:18
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github-actions bot commented Jun 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a2ecdcb

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • 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: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-10 14:20:39

@asp8200 asp8200 merged commit 54b3b08 into nf-core:dev Jun 10, 2024
8 checks passed
@asp8200 asp8200 deleted the update_usage_md branch June 10, 2024 17:14
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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