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Important! Template update for nf-core/tools v3.0.2 #103

Merged
merged 6 commits into from
Oct 29, 2024
Merged

Important! Template update for nf-core/tools v3.0.2 #103

merged 6 commits into from
Oct 29, 2024

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nf-core-bot
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Version 3.0.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.0.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.0.2 release page.

@nf-core-bot nf-core-bot mentioned this pull request Oct 11, 2024
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@scwatts
Merge branch 'dev' into nf-core-template-merge-3.0.2
8db1916
@scwatts
Rename variable used for HMF genomes base path
906d9a0
@scwatts
Add addition reference genome parameters to schema
5f5787f 
Triggers appearence of these important parameters in the startup display
text to show the configured values.
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github-actions bot commented Oct 28, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5f5787f

+| ✅ 194 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  14 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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_genome_gtf 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 3.0.2
  • Run at 2024-10-28 06:18:28

@scwatts scwatts requested a review from charlesshale October 28, 2024 07:23
@scwatts scwatts merged commit b4ca6b3 into dev Oct 29, 2024
5 checks passed
@scwatts scwatts deleted the nf-core-template-merge-3.0.2 branch October 29, 2024 08:40
@scwatts scwatts mentioned this pull request Dec 11, 2024
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@charlesshale charlesshale charlesshale approved these changes

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@nf-core-bot @charlesshale @scwatts