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Test refgenie CI - DO NOT MERGE #53

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TEST - DO NOT MERGE

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github-actions bot commented Dec 22, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 1a9d9b5

+| ✅ 156 tests passed       |+
!| ❗  22 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/workflows/linting.yml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.0'
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
  • 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 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in testpipeline.nf: Add all file path parameters for the pipeline to the list below
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.8.dev0
  • Run at 2023-01-12 13:42:43

@nf-core nf-core deleted a comment from github-actions bot Dec 22, 2022
@nf-core nf-core deleted a comment from github-actions bot Dec 22, 2022
@mirpedrol mirpedrol mentioned this pull request Dec 22, 2022
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@nf-core nf-core deleted a comment from github-actions bot Jan 12, 2023
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genomes.conf file was manually modified

The file containing URLs to reference genomes must be managed by Refgenie
To fix this CI test, please run:

  • Install refgenie: pip install refgenie
  • Populate genome URLs: refgenie populater --file <PIPELINE_DIR>/conf/genomes.config.tpl > <PIPELINE_DIR>/conf/genomes.config

Once you push these changes the test should pass, and you can hide this comment 👍

Thanks again for your contribution!

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3 participants
@mirpedrol @ggabernet @mashehu