test: fixing the default nf-test by kristinebilgrav · Pull Request #26 · Clinical-Genomics/oncorefiner

kristinebilgrav · 2026-02-24T13:08:34Z

Closes #15

Fixes the default nf-test, adding snaphot with software versions, variants in the VCFs, paths and file names.

PR checklist

github-actions · 2026-02-24T13:10:25Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 7c60c22

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗  28 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: TODO nf-core:
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)
pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
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 nextflow.config: Specify any additional parameters here
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
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!
schema_description - Ungrouped param in schema: snv_vcf
schema_description - Ungrouped param in schema: sv_vcf
schema_description - Ungrouped param in schema: custom_extra_files
local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - actions_awstest
actions_awsfulltest - actions_awsfulltest
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-oncorefiner_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-oncorefiner_logo_light.png
files_exist - File found: docs/images/nf-core-oncorefiner_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-oncorefiner_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowOncorefiner.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with Clinical-Genomics/
nextflow_config - Config variable manifest.homePage began with https://github.com/Clinical-Genomics/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.0.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.genome= GRCh38
nextflow_config - Config default value correct: params.vep_cache_version= 112
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/Clinical-Genomics/test-datasets/refs/heads/oncorefiner/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 25.10.0, Config: 25.10.0
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: add_pr_checklist_comment.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: conventional_pr_title.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: update_changelog.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBLVEP_SNV found in conf/modules.config and Nextflow scripts.
modules_config - VCFANNO found in conf/modules.config and Nextflow scripts.
modules_config - RESEARCH_FILTERING found in conf/modules.config and Nextflow scripts.
modules_config - CLINICAL_FILTERING found in conf/modules.config and Nextflow scripts.
modules_config - SVDB_QUERY_DB found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBLVEP_SV found in conf/modules.config and Nextflow scripts.
modules_config - RESEARCH_FILTERING_SV found in conf/modules.config and Nextflow scripts.
modules_config - CLINICAL_FILTERING_SV found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-10 16:09:01

fellen31

Awesome!

.github/workflows/ci.yml

.github/workflows/nf-test.yml

tests/nextflow.config

tests/default.nf.test.snap

beatrizsavinhas

The default test is finally passing, without referring to local file paths!! Much better, well done!!! 🌟

However, from reading the description of the issue and PR it is not clear to me what changes are intended to be introduced here and what is the reasoning behind these choices. So I have left a lot of comments asking "why?". 😅
As far as I understand, 2 things are being done at the same time here:

Update the default nf-test
Modify the CI checks for nf-tests

Could you please fill in the descriptions and add explanations for the changes? 🙂

.github/workflows/ci.yml

.github/workflows/nf-test.yml

tests/default.nf.test

tests/default.nf.test.snap

tests/nextflow.config

CHANGELOG.md

nextflow.config

…r into fix-testing

beatrizsavinhas

Nice! 🌟
Strange that there is no output for stable_path in the snapshot, though. Could you check that?
Also, I think the title (and if possible descriptions) should be updated. This PR is now fixing the default test only.

nextflow.config

tests/nextflow.config

tests/default.nf.test.snap

CHANGELOG.md

tests/default.nf.test

tests/default.nf.test.snap

beatrizsavinhas

Looks great! 🌟

adding nf-test

b5296b9

kristinebilgrav added 5 commits February 24, 2026 14:29

testing nf-test.yml

b5d6278

fixing action trigger

326c308

removing CI test

733eed8

updating snap and configs

4eb09bf

updating snapshot

cddc93a

kristinebilgrav changed the title ~~Adding nf-test~~ test: Adding nf-test Mar 2, 2026

kristinebilgrav and others added 5 commits March 2, 2026 15:39

Merge branch 'dev' into fix-testing

57d2391

pre-commit and upating changelog

8f09709

adding nftignore to ignore linting

980ce0b

adding gitignore to ignore linting

cf2cb72

updating test to summarize vcf

46bbf63

kristinebilgrav marked this pull request as ready for review March 3, 2026 14:49

kristinebilgrav requested a review from a team as a code owner March 3, 2026 14:49

fellen31 reviewed Mar 4, 2026

View reviewed changes

.github/workflows/ci.yml Outdated Show resolved Hide resolved

.github/workflows/nf-test.yml Show resolved Hide resolved

tests/nextflow.config Outdated Show resolved Hide resolved

tests/nextflow.config Outdated Show resolved Hide resolved

tests/default.nf.test.snap Show resolved Hide resolved

beatrizsavinhas requested changes Mar 4, 2026

View reviewed changes

beatrizsavinhas mentioned this pull request Mar 5, 2026

Software version not collected #31

Closed

3 tasks

fixing link to nfcore test data

bbe1618

This was referenced Mar 5, 2026

fix: prepare references config not being used #36

Merged

fix: Refactor .nf-core.yml and update template #35

Merged

kristinebilgrav and others added 8 commits March 9, 2026 11:36

update

27c74bc

updating according to review

a25a0e6

Merge branch 'dev' into fix-testing

2b4770a

Merge branch 'dev' into fix-testing

53e8cb6

updating snapshot

7552a3f

Merge branch 'fix-testing' of github.com:Clinical-Genomics/oncorefine…

8bf4670

…r into fix-testing

fixing some errors introduced

4584f87

fixing comment

3ec536a

kristinebilgrav requested a review from beatrizsavinhas March 10, 2026 14:34

beatrizsavinhas reviewed Mar 10, 2026

View reviewed changes

kristinebilgrav changed the title ~~test: Adding nf-test~~ test: fixing the default nf-test Mar 10, 2026

kristinebilgrav and others added 2 commits March 10, 2026 17:05

small fixes

cef155b

Merge branch 'dev' into fix-testing

7c60c22

beatrizsavinhas approved these changes Mar 11, 2026

View reviewed changes

kristinebilgrav merged commit 71d30ef into dev Mar 11, 2026
8 checks passed

kristinebilgrav deleted the fix-testing branch March 11, 2026 08:14

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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kristinebilgrav commented Feb 24, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

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