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Replaced local mindagap/duplicatefinder with nf-core module. #32

Merged
merged 3 commits into from
Dec 4, 2023
Merged

Replaced local mindagap/duplicatefinder with nf-core module. #32

merged 3 commits into from
Dec 4, 2023

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FloWuenne
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PR checklist

This PR replaces the local mindagap/duplicatefinder module with the nf-core one, installed using nf-core tools.

  • 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/molkart 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 Dec 2, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cdabd16

+| ✅ 158 tests passed       |+
!| ❗  10 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 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-04 09:40:34

kbestak
kbestak approved these changes Dec 4, 2023
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@kbestak kbestak left a comment

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LGTM 🚀

@kbestak kbestak merged commit 4acfb71 into dev Dec 4, 2023
6 checks passed
@FloWuenne FloWuenne deleted the duplicatefinder_patch branch December 6, 2023 09:00
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@kbestak kbestak kbestak approved these changes

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@FloWuenne @kbestak