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Fix Lint & Update latest modules #102

Merged
merged 2 commits into from Jun 8, 2022
Merged

Fix Lint & Update latest modules #102

merged 2 commits into from Jun 8, 2022

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apeltzer
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@apeltzer apeltzer commented Jun 8, 2022 •
edited

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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).

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apeltzer commented Jun 8, 2022

@nf-core-bot fix-linting

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apeltzer commented Jun 8, 2022

@nf-core-bot fix linting

@apeltzer apeltzer changed the title Fix Linting Fix Lint & Update latest modules Jun 8, 2022
@apeltzer apeltzer requested a review from fmalmeida June 8, 2022 09:19
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apeltzer commented Jun 8, 2022

@fmalmeida - this should now fix all linting issues, also updated modules from nf-core/modules directly to get rid of the issue that these were affected / changed from the upstream version.

We should check that all runs smoothly, maybe also locally before merging this to dev and then get another PR in with the AWS_FUll test.

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github-actions bot commented Jun 8, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a664665

+| ✅ 147 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-08 09:19:59

@apeltzer apeltzer merged commit 696113d into dev Jun 8, 2022
@apeltzer apeltzer deleted the fix-lint branch June 8, 2022 09:45
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@fmalmeida fmalmeida Awaiting requested review from fmalmeida

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