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Apply the fourth set of reviewer recommendations #67

Merged
merged 6 commits into from
Jul 17, 2024
Merged

Apply the fourth set of reviewer recommendations #67

merged 6 commits into from
Jul 17, 2024

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scwatts
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@scwatts scwatts commented Jul 17, 2024

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@scwatts scwatts requested a review from charlesshale July 17, 2024 06:28
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github-actions bot commented Jul 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit feca359

+| ✅ 177 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  14 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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_params - Schema param panel not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-17 08:17:13

@scwatts scwatts mentioned this pull request Jul 17, 2024
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SPPearce
SPPearce approved these changes Jul 17, 2024
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@scwatts @SPPearce
Apply typo correction
feca359 
Co-authored-by: Simon Pearce <[email protected]>
@scwatts scwatts merged commit b9ed09e into dev Jul 17, 2024
4 checks passed
@scwatts scwatts deleted the initial-release-review-changes branch July 17, 2024 08:22
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@SPPearce SPPearce SPPearce approved these changes

@charlesshale charlesshale Awaiting requested review from charlesshale

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@scwatts @SPPearce