Update/nf test/nextflow v.25.10.4 by sgsutcliffe · Pull Request #49 · phac-nml/snvphylnfc

sgsutcliffe · 2026-03-19T17:22:51Z

Updated the nf-test in github actions to use nextflow version 25.10.4 instead of latest to confirm compatibility.

github-actions · 2026-03-19T17:26:28Z

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

Posted for pipeline commit cabeb4a

+| ✅ 157 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ 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: 2.4.0
readme - README did not have an nf-core template version badge.

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-snvphylnfc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-snvphylnfc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-snvphylnfc_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/WorkflowSnvphylnfc.groovy
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: ro-crate-metadata.json
files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: .github/actions/get-shards/action.yml
files_exist - File is ignored: .github/actions/nf-test/action.yml
files_exist - File is ignored: tests/default.nf.test
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.max_cpus
nf_test_content - 'nf-test.config' checking ignored
files_unchanged - Required pipeline config not found - {'manifest.contributors'}
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/snvphylnfc/snvphylnfc/.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/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: 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-snvphylnfc_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.max_samples= 0
nextflow_config - Config default value correct: params.metadata_1_header= metadata_1
nextflow_config - Config default value correct: params.metadata_2_header= metadata_2
nextflow_config - Config default value correct: params.metadata_3_header= metadata_3
nextflow_config - Config default value correct: params.metadata_4_header= metadata_4
nextflow_config - Config default value correct: params.metadata_5_header= metadata_5
nextflow_config - Config default value correct: params.metadata_6_header= metadata_6
nextflow_config - Config default value correct: params.metadata_7_header= metadata_7
nextflow_config - Config default value correct: params.metadata_8_header= metadata_8
nextflow_config - Config default value correct: params.metadata_9_header= metadata_9
nextflow_config - Config default value correct: params.metadata_10_header= metadata_10
nextflow_config - Config default value correct: params.metadata_11_header= metadata_11
nextflow_config - Config default value correct: params.metadata_12_header= metadata_12
nextflow_config - Config default value correct: params.metadata_13_header= metadata_13
nextflow_config - Config default value correct: params.metadata_14_header= metadata_14
nextflow_config - Config default value correct: params.metadata_15_header= metadata_15
nextflow_config - Config default value correct: params.metadata_16_header= metadata_16
nextflow_config - Config default value correct: params.min_coverage_depth= 15
nextflow_config - Config default value correct: params.min_mapping_percent_cov= 80
nextflow_config - Config default value correct: params.min_mean_mapping_quality= 30
nextflow_config - Config default value correct: params.window_size= 500
nextflow_config - Config default value correct: params.density_threshold= 2
nextflow_config - Config default value correct: params.snv_abundance_ratio= 0.75
nextflow_config - Config default value correct: params.min_repeat_length= 150
nextflow_config - Config default value correct: params.min_repeat_pid= 90
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/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' contains outdir parameter
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
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: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.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
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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/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 - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - CONSOLIDATE_BCFS 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

Run details

nf-core/tools version 3.5.2
Run at 2026-03-20 20:11:20

sgsutcliffe added 2 commits March 19, 2026 13:19

Update NXF_VER to version 25.10.4

29190b6

Commented line from nextflow.config to trigger nf-test

49937ab

sgsutcliffe added 4 commits March 20, 2026 15:37

Update documentation for github action nextflow v.25.10.4

4777903

Remove conda profile

ec94ff9

Remove flakey tests in snap

a956261

new prettier

cabeb4a

apetkau approved these changes Mar 20, 2026

View reviewed changes

sgsutcliffe merged commit f1c2ec6 into dev Mar 20, 2026
18 checks passed

sgsutcliffe deleted the update/nf-test/nextflow-v.25.10.4 branch March 20, 2026 20:37

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Update/nf test/nextflow v.25.10.4#49

Update/nf test/nextflow v.25.10.4#49
sgsutcliffe merged 6 commits into
devfrom
update/nf-test/nextflow-v.25.10.4

sgsutcliffe commented Mar 19, 2026

Uh oh!

github-actions Bot commented Mar 19, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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sgsutcliffe commented Mar 19, 2026

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github-actions Bot commented Mar 19, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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Reviewers

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Labels

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Development

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github-actions Bot commented Mar 19, 2026 •

edited

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