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refactor: split out pixelator dependency in CHECK_SAMPLESHEET #58

Merged
merged 1 commit into from
Aug 10, 2023
Merged

refactor: split out pixelator dependency in CHECK_SAMPLESHEET #58

merged 1 commit into from
Aug 10, 2023

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fbdtemme
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@fbdtemme fbdtemme commented Aug 9, 2023

As discussed here: https://github.com/PixelgenTechnologies/nf-core-pixelator/pull/57#discussion_r1288515954

Split out pixelator use from CHECK_SAMPLESHEET.
The possible design options are now an extra file input to CHECK_SAMPLESHEET.

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github-actions bot commented Aug 9, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f177cf7

+| ✅ 151 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  12 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: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • 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
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-10 08:45:01

@fbdtemme fbdtemme mentioned this pull request Aug 10, 2023
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@fbdtemme fbdtemme force-pushed the split-samplesheet-check branch from 0774c8c to f177cf7 Compare August 10, 2023 08:43
@fbdtemme fbdtemme merged commit f177cf7 into dev Aug 10, 2023
@fbdtemme fbdtemme deleted the split-samplesheet-check branch August 10, 2023 12:58
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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