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Add test configuration #7

Merged
merged 6 commits into from
Apr 29, 2024
Merged

Add test configuration #7

merged 6 commits into from
Apr 29, 2024

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nictru
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@nictru nictru commented Apr 28, 2024

This is important for CI tests.

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github-actions bot commented Apr 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7ed9b2b

+| ✅ 186 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  13 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • 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!
  • 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:

  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/base.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/configuration.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/macros.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/network.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/snp.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tf.html
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/tfactivity/tfactivity/modules/local/report/create/app/templates/tg.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-29 07:05:04

@nictru
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nictru commented Apr 28, 2024

Before this can be merged, the test data must be merged from my fork into the official repo

@nictru nictru mentioned this pull request Apr 29, 2024
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@nictru nictru marked this pull request as ready for review April 29, 2024 07:19
@nictru nictru requested a review from LeonHafner April 29, 2024 07:19
LeonHafner
LeonHafner approved these changes Apr 29, 2024
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Looks good!

@nictru nictru merged commit cb4cb9e into dev Apr 29, 2024
4 checks passed
@nictru nictru deleted the test-config branch April 29, 2024 08:46
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@LeonHafner LeonHafner LeonHafner approved these changes

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