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Move protocols to config profile(s) #364

Merged
merged 4 commits into from
Jul 31, 2024
Merged

Move protocols to config profile(s) #364

merged 4 commits into from
Jul 31, 2024

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apeltzer
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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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@apeltzer
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As discussed with @lpantano @christopher-mohr @greeco @apeltzer - we will move the protocols to distinct profiles and then can even have testcases for different protocols.

Ditching the parameters from the utils subworkflow as it seems like these do not get passed to other subworkflows.

@apeltzer
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Maybe fixing #351

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github-actions bot commented Jul 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d908088

+| ✅ 213 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • schema_description - No description provided in schema for parameter: protocol

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-30 15:28:48

@apeltzer apeltzer mentioned this pull request Jul 30, 2024
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@apeltzer apeltzer changed the title WIP - move protocols to config profile(s) Move protocols to config profile(s) Jul 30, 2024
@lpantano
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handling this as well #362

@apeltzer apeltzer merged commit 374ec02 into dev Jul 31, 2024
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@apeltzer apeltzer deleted the move-protocols-to-profiles branch July 31, 2024 07:03
This was referenced Jul 31, 2024
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@lpantano lpantano lpantano approved these changes

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@apeltzer @lpantano