Update/nf core/nextflow v.25.10.4 by sgsutcliffe · Pull Request #76 · phac-nml/gasclustering

sgsutcliffe · 2026-03-19T17:43:25Z

Adding 25.10.4 nextflow to github action nf-test to confirm compatibility

Add comment to nextflow.config for clarity

github-actions · 2026-03-19T17:44:54Z

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

Posted for pipeline commit 81f8cd2

+| ✅ 167 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: 0.8.3
readme - README did not have an nf-core template version badge.

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-gasclustering_logo_light.png
files_exist - File is ignored: docs/images/nf-core-gasclustering_logo_light.png
files_exist - File is ignored: docs/images/nf-core-gasclustering_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/WorkflowGasclustering.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/gasclustering/gasclustering/.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-gasclustering_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.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.metadata_17_header= metadata_17
nextflow_config - Config default value correct: params.metadata_18_header= metadata_18
nextflow_config - Config default value correct: params.metadata_19_header= metadata_19
nextflow_config - Config default value correct: params.metadata_20_header= metadata_20
nextflow_config - Config default value correct: params.metadata_21_header= metadata_21
nextflow_config - Config default value correct: params.metadata_22_header= metadata_22
nextflow_config - Config default value correct: params.metadata_23_header= metadata_23
nextflow_config - Config default value correct: params.metadata_24_header= metadata_24
nextflow_config - Config default value correct: params.pd_outfmt= matrix
nextflow_config - Config default value correct: params.pd_distm= hamming
nextflow_config - Config default value correct: params.pd_missing_threshold= 1.0
nextflow_config - Config default value correct: params.pd_sample_quality_threshold= 1.0
nextflow_config - Config default value correct: params.pd_file_type= text
nextflow_config - Config default value correct: params.gm_thresholds= 10,5,0
nextflow_config - Config default value correct: params.gm_method= average
nextflow_config - Config default value correct: params.gm_delimiter= .
nextflow_config - Config default value correct: params.gm_tree_distances= cophenetic
nextflow_config - Config default value correct: params.gm_sort_matrix= false
nextflow_config - Config default value correct: params.batch_size= 100
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
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 - LOCIDEX_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - LOCIDEX_CONCAT found in conf/modules.config and Nextflow scripts.
modules_config - GAS_MCLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - PROFILE_DISTS found in conf/modules.config and Nextflow scripts.
modules_config - ARBOR_VIEW 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: 3.5.2

Run details

nf-core/tools version 3.5.2
Run at 2026-03-23 19:05:00

apetkau · 2026-03-23T18:50:28Z

 env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.2"


It looks like some of the versions (NFT_VER and actions/checkout) got downgraded here. Can you change back to the more recent versions?

I think the template I was copying was behind gasclustering, so I reverted to the version in main and then manually made the changes.

…test-everything

sgsutcliffe added 2 commits March 19, 2026 13:40

Update NXF_VER to version 25.10.4

d958c9d

Add comment to nextflow.config

e2d2df6

Add comment to nextflow.config for clarity

sgsutcliffe added 2 commits March 20, 2026 16:46

Final github action change

ebb79e0

add nf-test.yml to triggers

3a3e972

apetkau self-requested a review March 23, 2026 18:49

apetkau approved these changes Mar 23, 2026

View reviewed changes

Revert nf-test.yml except the nextflow version 25.10.4 in place of la…

81f8cd2

…test-everything

sgsutcliffe merged commit f79d5ea into dev Mar 23, 2026
12 checks passed

sgsutcliffe deleted the update/nf-core/nextflow-v.25.10.4 branch March 23, 2026 19:24

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Update/nf core/nextflow v.25.10.4#76

Update/nf core/nextflow v.25.10.4#76
sgsutcliffe merged 5 commits into
devfrom
update/nf-core/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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apetkau Mar 23, 2026

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sgsutcliffe Mar 23, 2026

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sgsutcliffe commented Mar 19, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

apetkau Mar 23, 2026

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sgsutcliffe Mar 23, 2026

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github-actions Bot commented Mar 19, 2026 •

edited

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