STRY0019104 - Test against GSP version of Nextflow in GitHub CI for all pipelines #34

apetkau · 2025-10-01T18:13:48Z

Adding GitHub CI tests against Nextflow 24.10.3
Some minor updates to GitHub actions and .nf-core.yml to better match latest nf-core template.

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
CHANGELOG.md is updated.

github-actions · 2025-10-01T18:18:01Z

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

Posted for pipeline commit dbb1aa8

+| ✅ 141 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
nextflow_config - Config manifest.version should end in dev: 1.0.4
readme - README did not have an nf-core template version badge.
local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-iridanextexample_logo_light.png
files_exist - File is ignored: docs/images/nf-core-iridanextexample_logo_light.png
files_exist - File is ignored: docs/images/nf-core-iridanextexample_logo_dark.png
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/WorkflowIridanextexample.groovy
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: ro-crate-metadata.json
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.max_cpus
files_unchanged - Required pipeline config not found - {'manifest.contributors'}
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/iridanextexample/iridanextexample/.github/workflows/awstest.yml
actions_awsfulltest - actions_awsfulltest
pipeline_name_conventions - pipeline_name_conventions
rocrate_readme_sync - ro-crate-metadata.json not found

✅ 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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: conf/igenomes.config
files_exist - File found: modules.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-iridanextexample_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/Workflow.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-validation plugin
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: 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 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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.project_name= assembly
nextflow_config - Config default value correct: params.assembler= stub
nextflow_config - Config default value correct: params.random_seed= 1
nextflow_config - Config default value correct: params.max_cpus= 4
nextflow_config - Config default value correct: params.max_memory= 2.GB
nextflow_config - Config default value correct: params.max_time= 1.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
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
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 Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
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: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - ASSEMBLY_STUB found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - IRIDA_NEXT_OUTPUT found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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: 3.3.2

Run details

nf-core/tools version 3.3.2
Run at 2025-10-07 21:43:47

apetkau added 2 commits October 1, 2025 13:12

Updating tests for nextflow 24.10.3

7442687

Fixed schema URLs

f08e505

apetkau added 11 commits October 7, 2025 16:13

Updated github ci workflows

7da73cd

Updated nf-core and nf-test configs

a7b7ffb

Updated nextflow versions to test

5bf09c6

Updated tests

7864d20

Fixed up some test configs

1631468

Updated/fixed tests

28dd55a

Updated changelog and nf-core linting

9f6bafa

Updated some text in github workflow

3107593

More fixes to github workflows

4eb4014

Removed fix_linting github workflow

fbb565d

Add extra newline to default.nf.test

dbb1aa8

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STRY0019104 - Test against GSP version of Nextflow in GitHub CI for all pipelines #34

STRY0019104 - Test against GSP version of Nextflow in GitHub CI for all pipelines #34

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apetkau commented Oct 1, 2025 •

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github-actions bot commented Oct 1, 2025 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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STRY0019104 - Test against GSP version of Nextflow in GitHub CI for all pipelines #34

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PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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apetkau commented Oct 1, 2025 •

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