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Fix for hidden output docs #232

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Fix for hidden output docs #232

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jpcartailler
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Issue

  • There is an open <details markdown="1"> tag in the last working section (### 4.3), but no closing tag.
  • Then section 5 starts. Then, right after ###6.5 starts, there is dangling closing tag </details>
  • Then section 7 begins

Fix
Move tag to appropriate location

PR checklist

  • This comment contains a description of changes (with reason).
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated

@github-actions GitHub Actions
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github-actions bot commented Feb 28, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 028f027

+| ✅ 196 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   8 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowCutandrun.groovy
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.2.2
  • pipeline_todos - TODO string in WorkflowCutandrun.groovy: Optionally add in-text citation tools to this list.
  • 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:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-28 09:21:03

@chris-cheshire
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Hi @jpcartailler, sorry for taking so long to get to this, I have been away on Paternity leave. Could you fix the tests and I can merge?

@jpcartailler
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Thanks @chris-cheshire and no worries, being a dad is way more important.

I'm a little puzzled by the errors to be honest. I was just modifying two .md files, but see errors related to the following:

[files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/Utils.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/WorkflowMain.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/NfcoreTemplate.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/WorkflowCutandrun.groovy
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/branch.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/linting_comment.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/linting.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - pyproject.toml does not match the template

Any thoughts or guidance? TY

@chris-cheshire
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Damn i think I need to upgrade the pipeline to pass the new nf-core tools spec. Bear with me, I will update the pipeline and then you will need to pull from dev

@jpcartailler
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Thanks @chris-cheshire - is there anything for me to try yet?

@chris-cheshire
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Not yet no, this needs quite a large update I am afraid. Nf-core have removed all the groovy libs in favour of plugins so its a substantial code change

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@jpcartailler @chris-cheshire