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Enhancement/adding unit testing #128

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Enhancement/adding unit testing #128

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@rhassaine rhassaine commented Feb 4, 2025 •
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PR checklist

Adding nf-tests on the module-level to meet nf-core requirements

  • 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 necessary, also make a PR on the nf-core/oncoanalyser branch on the [nf-core/test-datasets]*(https://github.com/nf-core/test-datasets) repository.
  • Make sure your code lints (nf-core lint).

*Currently working with locally-staged resources (pending update)

@rhassaine rhassaine requested a review from scwatts February 4, 2025 10:24
@rhassaine rhassaine self-assigned this Feb 4, 2025
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Feb 4, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 6df1caf

+| ✅ 200 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  18 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

❗ 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 fastp_umi_location not found from nextflow config
  • schema_params - Schema param fastp_umi_length not found from nextflow config
  • schema_params - Schema param fastp_umi_skip not found from nextflow config
  • schema_params - Schema param markdups_umi_duplex_delim 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 2025-02-05 16:04:14

@rhassaine rhassaine marked this pull request as draft February 4, 2025 12:02
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@scwatts scwatts Awaiting requested review from scwatts

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