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nf-test: utils_nfcore_rnaseq_pipeline tests #1235

Merged
merged 8 commits into from
Mar 6, 2024
Merged

nf-test: utils_nfcore_rnaseq_pipeline tests #1235

merged 8 commits into from
Mar 6, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Mar 6, 2024 •
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  • Add nf-tests for nf-core/rnaseq utility functions
  • Adds tests for nf-core/rnaseq utility subworkflows
  • Makes nextflow_schema.json a parameter for both subworkflows so it can be set correctly in the test and improves scoping of the subworkflows.
  • Subworkflow tests only check for correct running right now - need to refine them in future.
  • Changes function name from validateInputSamplesheet to checkSamplesAreConsistent which more accurately reflects what it is doing.

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 (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).

@adamrtalbot
Add nf-tests for nf-core/rnaseq utility functions
18fcdbd 
Changes:
 - Change function name from validateInputSamplesheet to checkSamplesAreConsistent to accurately reflect what the function is doing
 - Add nf-tests for all functions in UTILS_NFCORE_RNASEQ_PIPELINE
@adamrtalbot
Adds tests for nf-core/rnaseq utility subworkflows
c988ce0 
Changes:
 - Makes nextflow_schema.json a parameter so we can actually set it. Not exposed right now but will be.
 - Adds basic tests that check for correct running only. Defaults to lots of stuff off.

We should extend this to check for more things but we're in a rush right now.
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github-actions bot commented Mar 6, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f8f493c

+| ✅ 169 tests passed       |+
#| ❔   8 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 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!
  • 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

❔ 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_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 2024-03-06 18:02:58

@adamrtalbot adamrtalbot mentioned this pull request Mar 6, 2024
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pinin4fjords
pinin4fjords approved these changes Mar 6, 2024
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Chunky amount of work! Just skimmed and spotted a lingering println, but that's all.

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf Outdated
@@ -507,6 +509,7 @@ def getStarPercentMapped(params, align_log) {
align_log.eachLine { line ->
def matcher = line =~ pattern
if (matcher) {
println matcher[0][1].toFloat()
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Assume this is going?

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Blast!

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Fixed now.

@adamrtalbot adamrtalbot merged commit cb26b69 into nf-core:dev Mar 6, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@adamrtalbot @pinin4fjords