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Template merge v2.8 #42

Merged
merged 10 commits into from
May 11, 2023
Merged

Template merge v2.8 #42

merged 10 commits into from
May 11, 2023

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nvnieuwk
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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
  • 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).

@github-actions
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

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

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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github-actions bot commented May 11, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 48bed31

+| ✅ 125 tests passed       |+
#| ❔  25 tests were ignored |#
!| ❗  15 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 methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 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.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 output.md: Write this documentation describing your workflow's output
  • 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.
  • system_exit - System.exit in WorkflowNfCmggStructural.groovy: System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowNfCmggStructural.groovy: System.exit(1) [line 74]

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nf-cmgg-structural_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-cmgg-structural_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-cmgg-structural_logo_dark.png
  • files_exist - File is ignored: assets/nf-core-nf-cmgg-structural_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-cmgg-structural_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nf-cmgg-structural_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: lib/WorkflowNf-cmgg-structural.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File does not exist: assets/nf-core-nf-cmgg-structural_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-nf-cmgg-structural_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-nf-cmgg-structural_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-cmgg-structural/nf-cmgg-structural/.github/workflows/awstest.yml
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-11 14:12:49

@nvnieuwk nvnieuwk merged commit dbb159b into update-annotation May 11, 2023
@nvnieuwk nvnieuwk deleted the template-v2.8 branch May 11, 2023 14:26
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@nvnieuwk