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Tiny update of docs #490

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Tiny update of docs #490

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asp8200
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@asp8200 asp8200 commented Jun 11, 2024 •
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Some nf run-cmds contained the -profile flag twice:

nextflow run nf-core/rnafusion -r 3.0.2 -profile test -profile docker --outdir results -stub
Can only specify option -profile once. -- Check the available commands and options and syntax with 'help'

https://nfcore.slack.com/archives/CGB1CL0SC/p1718100188436269

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/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • 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 Jun 11, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 488dc82

+| ✅ 207 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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!

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-11 12:06:12

@asp8200
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asp8200 commented Jun 11, 2024

Problem with missing secrets for PR from fork. Closing this.

@asp8200 asp8200 closed this Jun 11, 2024
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