Fix singularity ci tests by Aratz · Pull Request #245 · nf-core/pixelator

Aratz · 2026-08-20T06:20:09Z

For some reason, the setup-apptainer step in the nf-test action was bumped back to the previous version, causing the tests to fail in #244 . This PR sets it back to the latest version. This is the same setup as eg nf-core/seqinspector and sarek.

PR checklist

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

github-actions · 2026-08-20T06:20:56Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-08-20T06:22:44Z

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

Posted for pipeline commit ee3337d

+| ✅ 233 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 5.0.1

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: tests/default.nf.test
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
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/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/pr-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-pixelator_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/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-pixelator_logo_light.png
files_exist - File found: docs/images/nf-core-pixelator_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: main.nf
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-pixelator_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/WorkflowPixelator.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 nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
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.pna_amplicon_mismatches= 0.1
nextflow_config - Config default value correct: params.pna_amplicon_remove_polyg= true
nextflow_config - Config default value correct: params.pna_amplicon_quality_cutoff= 20
nextflow_config - Config default value correct: params.pna_amplicon_low_complexity_filter= true
nextflow_config - Config default value correct: params.pna_amplicon_low_complexity_threshold= 0.8
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter= true
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter_min_overlap= 8
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter_error_rate= 0.1
nextflow_config - Config default value correct: params.pna_demux_mismatches= 1
nextflow_config - Config default value correct: params.pna_demux_output_chunk_reads= 50M
nextflow_config - Config default value correct: params.pna_demux_output_max_chunks= 8
nextflow_config - Config default value correct: params.pna_demux_strategy= independent
nextflow_config - Config default value correct: params.pna_collapse_algorithm= directional
nextflow_config - Config default value correct: params.pna_collapse_mismatches= 2
nextflow_config - Config default value correct: params.pna_graph_multiplet_recovery= true
nextflow_config - Config default value correct: params.pna_graph_initial_stage_leiden_resolution= 1.0
nextflow_config - Config default value correct: params.pna_graph_refinement_stage_leiden_resolution= 0.5
nextflow_config - Config default value correct: params.pna_graph_edge_cycle_verification= true
nextflow_config - Config default value correct: params.pna_graph_min_count= 1.0
nextflow_config - Config default value correct: params.pna_graph_max_refinement_recursion_depth= 3
nextflow_config - Config default value correct: params.pna_graph_initial_stage_max_edges_to_remove= 10
nextflow_config - Config default value correct: params.pna_graph_refinement_stage_max_edges_to_remove= 20
nextflow_config - Config default value correct: params.pna_graph_component_size_min_threshold= 8000
nextflow_config - Config default value correct: params.pna_graph_component_size_max_threshold= 1000000
nextflow_config - Config default value correct: params.pna_sample_calling_remove_incompatible= true
nextflow_config - Config default value correct: params.pna_sample_calling_enrichment_threshold= 10.0
nextflow_config - Config default value correct: params.pna_denoise_pval_threshold= 0.05
nextflow_config - Config default value correct: params.pna_denoise_inflate_factor= 1.5
nextflow_config - Config default value correct: params.pna_denoise_run_ace_denoising= true
nextflow_config - Config default value correct: params.pna_denoise_ace_k= 3
nextflow_config - Config default value correct: params.pna_denoise_run_pls_denoising= true
nextflow_config - Config default value correct: params.pna_denoise_pls_score_threshold= -3.0
nextflow_config - Config default value correct: params.pna_analysis_compute_proximity= true
nextflow_config - Config default value correct: params.pna_analysis_compute_k_cores= true
nextflow_config - Config default value correct: params.pna_analysis_proximity_nbr_of_permutations= 100
nextflow_config - Config default value correct: params.pna_analysis_compute_svd_var_explained= true
nextflow_config - Config default value correct: params.pna_analysis_svd_nbr_of_pivots= 50
nextflow_config - Config default value correct: params.pna_layout_layout_algorithm= coarsened_pmds_3d
nextflow_config - Config default value correct: params.pna_layout_pmds_pivots= 50
nextflow_config - Config default value correct: params.pna_layout_wpmds_k= 5
nextflow_config - Config default value correct: params.save_json= true
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.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/e8950f260973a6778e2ff24988e12fd4474d60e1/
nextflow_config - Config default value correct: params.modules_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/
nf_test_content - 'tests/proxiome_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains modules_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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_dark.png matches the template
files_unchanged - docs/README.md 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
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
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
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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: release.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: post-release-sync.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 subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - PIXELATOR found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LIST_OPTIONS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ 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: 4.0.3
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 4.0.3
Run at 2026-08-20 06:38:56

This reverts commit f257d7f.

Aratz added 2 commits August 20, 2026 08:12

Temporarily allow singularity tests to run on dev

f257d7f

Bump setup-apptainer to latest

216b484

Aratz requested a review from a team as a code owner August 20, 2026 06:20

Aratz self-assigned this Aug 20, 2026

Aratz added 2 commits August 20, 2026 08:36

Revert "Temporarily allow singularity tests to run on dev"

04244ab

This reverts commit f257d7f.

Update changelog

ee3337d

johandahlberg approved these changes Aug 20, 2026

View reviewed changes

Aratz merged commit 81ed0ca into nf-core:dev Aug 20, 2026
21 checks passed

Aratz mentioned this pull request Aug 20, 2026

Release 5.0.1 #244

Merged

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Fix singularity ci tests - #245

Fix singularity ci tests#245
Aratz merged 4 commits into
nf-core:devfrom
Aratz:dev

Aratz commented Aug 20, 2026 •

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❗ Test warnings:

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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Aratz commented Aug 20, 2026 •

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