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Testing full pipeline #44

Merged
merged 11 commits into from
Oct 26, 2023
Merged

Testing full pipeline #44

merged 11 commits into from
Oct 26, 2023

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Lucpen
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@Lucpen Lucpen commented Oct 24, 2023

PR checklist

  • The pipeline should now work
  • 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
  • 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).

@Lucpen Lucpen requested a review from jemten as a code owner October 24, 2023 12:23
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github-actions bot commented Oct 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 71a93cd

+| ✅ 143 tests passed       |+
#| ❔ 252 tests were ignored |#
!| ❗  16 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 nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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
  • 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 tomte.nf: change this to use the plugin nf-validation
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-25 13:22:44

@Lucpen Lucpen added the Ready for review Ready for review label Oct 24, 2023
jemten
jemten reviewed Oct 25, 2023
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Nice work! So close now 😄

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@Lucpen Lucpen requested a review from jemten October 25, 2023 14:07
jemten
jemten approved these changes Oct 25, 2023
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🎉

@jemten jemten merged commit 2ecb56f into master Oct 26, 2023
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@jemten jemten deleted the testing_full_pipeline branch October 26, 2023 11:31
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