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Increase contents of default.main.nf.test.snap #1283

Merged
merged 6 commits into from
Apr 12, 2024
Merged

Increase contents of default.main.nf.test.snap #1283

merged 6 commits into from
Apr 12, 2024

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adamrtalbot
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Changes:

  • Adds output files to nf-test snapshot
  • Used files that are important for downstream analysis to ensure that the snapshot is useful for testing
  • Should help stability of pipeline

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/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test tests/ --verbose --profile +docker).
  • 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).

@adamrtalbot
Increase contents of default.main.nf.test.snap
2f42e75 
Changes:
 - Adds output files to nf-test snapshot
 - Used files that are important for downstream analysis to ensure that the snapshot is useful for testing
 - Should help stability of pipeline
@adamrtalbot
CHANGELOG
651c755
@adamrtalbot
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@pinin4fjords can you make sure the files for differentialabundance are in this snapshot?

laramiellindsey
laramiellindsey approved these changes Apr 10, 2024
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@laramiellindsey laramiellindsey left a comment

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LGTM

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github-actions bot commented Apr 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b903195

+| ✅ 167 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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
  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-11 15:02:42

@pinin4fjords
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@pinin4fjords can you make sure the files for differentialabundance are in this snapshot?

Unfortunately they're not. You'd need either the .gene_lengths.tsv AND the .gene_counts.tsv, or else the gene_counts_length_scaled.tsv.

But realise part of this is due to the snapshot issues.

@adamrtalbot adamrtalbot merged commit d129b5a into nf-core:dev Apr 12, 2024
20 checks passed
@adamrtalbot adamrtalbot deleted the increase_coverage_of_default_test_snapshot branch April 12, 2024 15:32
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@laramiellindsey laramiellindsey laramiellindsey approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

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@adamrtalbot @pinin4fjords @laramiellindsey