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Replacing local modules with nf-core equivalent #546

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Replacing local modules with nf-core equivalent #546

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CarsonJM
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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
  • If necessary, also make a PR on the nf-core/mag 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 --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).

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github-actions bot commented Nov 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6032501

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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 WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-30 00:59:58

@CarsonJM CarsonJM marked this pull request as draft November 30, 2023 18:14
@CarsonJM CarsonJM self-assigned this Nov 30, 2023
@CarsonJM CarsonJM changed the title Implementing nf-tests and replacing local modules with nf-core equivalent Replacing local modules with nf-core equivalent Nov 30, 2023
@CarsonJM CarsonJM closed this Nov 30, 2023
@CarsonJM CarsonJM deleted the nf-tests branch November 30, 2023 18:16
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