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Prevent pipeline fails from erroneous param validation when igenomes is used #433

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Prevent pipeline fails from erroneous param validation when igenomes is used #433

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JoseEspinosa
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See this slack thread

For the record, any include can not be before parameter assignation by getGenomeAttribute or otherwise it won't be solved before validation

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Nov 20, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 17c9afc

+| ✅ 234 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   7 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • schema_params - Default value for param skip_reporting invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all 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
  • schema_params - Schema param skip_reporting not found from nextflow config

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-20 15:28:19

@JoseEspinosa
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Close in favour of a clean PR

@JoseEspinosa JoseEspinosa deleted the fixes branch November 20, 2024 15:51
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@JoseEspinosa