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Add module tests with nf-test #110

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Add module tests with nf-test #110

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rhassaine
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@rhassaine rhassaine commented Nov 12, 2024 •
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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/oncoanalyser branch on the nf-core/test-datasets repository.
  • 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>).
  • 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).

@github-actions GitHub Actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @rhassaine,

It looks like this pull-request is has been made against the nf-core/oncoanalyser master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/oncoanalyser dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions GitHub Actions
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github-actions bot commented Nov 12, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 9268ed5

+| ✅ 194 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  14 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • nextflow_config - Config manifest.version should not contain dev for a release: 1.1.0dev
  • version_consistency - manifest.version was not numeric: 1.1.0dev!
  • included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ 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 2024-11-12 13:04:11

@rhassaine rhassaine self-assigned this Nov 12, 2024
@rhassaine rhassaine added the enhancement New feature or request label Nov 12, 2024
@rhassaine rhassaine changed the base branch from master to dev November 12, 2024 13:19
@scwatts scwatts changed the title Added amber module test Add module tests with nf-test Dec 4, 2024
@scwatts scwatts marked this pull request as draft December 4, 2024 22:13
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scwatts commented Dec 11, 2024

@rhassaine rhassaine closed this Feb 4, 2025
@rhassaine rhassaine deleted the add-amber-module-test branch February 4, 2025 10:25
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@rhassaine @scwatts