Important! Template update for nf-core/tools v4.2.1 by nf-core-bot · Pull Request #377 · nf-core/scdownstream

nf-core-bot · 2026-10-26T16:05:37Z

Version 4.2.1 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2026/tools-4_2_0

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-4.2.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see the template sync documentation.

For more information about this release of nf-core/tools, please see the v4.2.1 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

…-4.2.1

github-actions · 2026-10-27T16:25:29Z

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

Posted for pipeline commit 8638e9a

+| ✅ 331 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in CHANGELOG.md: ## v0.0.1dev - [unreleased replace with date on release ]
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
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.

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ 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-scdownstream_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-scdownstream_logo_light.png
files_exist - File found: docs/images/nf-core-scdownstream_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: .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-scdownstream_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/WorkflowScdownstream.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: manifest.diagram
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 manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config manifest.diagram file found: docs/images/metromap.svg
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 0.0.1dev
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.duplicate_var_resolution= sum
nextflow_config - Config default value correct: params.species= human
nextflow_config - Config default value correct: params.cell_cycle_scoring= true
nextflow_config - Config default value correct: params.ambient_correction= soupx
nextflow_config - Config default value correct: params.use_ambient_corrected_counts= false
nextflow_config - Config default value correct: params.doublet_detection= scdblfinder
nextflow_config - Config default value correct: params.doublet_detection_threshold= 1
nextflow_config - Config default value correct: params.doublet_removal= false
nextflow_config - Config default value correct: params.empty_droplet_removal= cellbender
nextflow_config - Config default value correct: params.emptydrops_lower= 100
nextflow_config - Config default value correct: params.emptydrops_fdr= 0.01
nextflow_config - Config default value correct: params.cellbender_epochs= 150
nextflow_config - Config default value correct: params.integration_methods= scvi
nextflow_config - Config default value correct: params.feature_selection= deviance
nextflow_config - Config default value correct: params.integration_n_features= 0
nextflow_config - Config default value correct: params.normalization_method= scran
nextflow_config - Config default value correct: params.scimilarity_model= https://zenodo.org/records/10685499/files/model_v1.1.tar.gz
nextflow_config - Config default value correct: params.base_label_col= label
nextflow_config - Config default value correct: params.base_condition_col= condition
nextflow_config - Config default value correct: params.base_donor_col= donor
nextflow_config - Config default value correct: params.integrate_per_label= false
nextflow_config - Config default value correct: params.clustering_resolutions= 0.25,0.5,1.0
nextflow_config - Config default value correct: params.tsne= false
nextflow_config - Config default value correct: params.cluster_global= true
nextflow_config - Config default value correct: params.memory_scale= 1
nextflow_config - Config default value correct: params.liana_n_perms= 1000
nextflow_config - Config default value correct: params.liana_subsample_strategy= stratified_obs
nextflow_config - Config default value correct: params.liana_subsample_seed= 42
nextflow_config - Config default value correct: params.cell2cell= false
nextflow_config - Config default value correct: params.cell2cell_seed= 42
nextflow_config - Config default value correct: params.scib= false
nextflow_config - Config default value correct: params.scib_subsample_strategy= stratified_label_batch
nextflow_config - Config default value correct: params.scib_subsample_seed= 42
nextflow_config - Config default value correct: params.scib_metric_profile= fast
nextflow_config - Config default value correct: params.de_methods= wilcoxon
nextflow_config - Config default value correct: params.scvi_n_latent= 30
nextflow_config - Config default value correct: params.scvi_n_hidden= 128
nextflow_config - Config default value correct: params.scvi_n_layers= 2
nextflow_config - Config default value correct: params.scvi_dispersion= gene
nextflow_config - Config default value correct: params.scvi_gene_likelihood= zinb
nextflow_config - Config default value correct: params.scvi_use_observed_lib_size= true
nextflow_config - Config default value correct: params.pseudobulk= false
nextflow_config - Config default value correct: params.pseudobulk_min_num_cells= 10
nextflow_config - Config default value correct: params.pseudobulk_min_total_counts= 1000
nextflow_config - Config default value correct: params.decoupler_resources= progeny,collectri
nextflow_config - Config default value correct: params.decoupler_method= ulm
nextflow_config - Config default value correct: params.decoupler_min_targets= 5
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/nf-core/test-datasets/4d8b9974c14cf11280d29bfe16f94e284793e499/
nf_test_content - 'tests/main_pipeline_sub.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_sub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_sub.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_sub_integrate_per_label.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_sub_integrate_per_label.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_sub_integrate_per_label.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_sub_integrate_per_label.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_emptydrops.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_emptydrops.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_emptydrops.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_extend.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_extend.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_extend.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_reference_mapping.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_reference_mapping.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_qc.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/params.nf.test' contains outdir parameter
nf_test_content - 'tests/params.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/params.nf.test' contains outdir parameter
nf_test_content - 'tests/params.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/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_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 - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE 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/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/pr-comment.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 - assets/nf-core-scdownstream_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scdownstream_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scdownstream_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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: 26.04.6, Config: 26.04.6
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: pr-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.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: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 a matching 'report_comment'.
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.
modules_config - conf/modules.config found and not ignored.
modules_config - COLLECT_SIZES found in conf/modules.config and Nextflow scripts.
modules_config - QC_RAW found in conf/modules.config and Nextflow scripts.
modules_config - QC_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - CELDA_DECONTX found in conf/modules.config and Nextflow scripts.
modules_config - SOUPX found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - SCVITOOLS_SOLO found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_SCRUBLET found in conf/modules.config and Nextflow scripts.
modules_config - DOUBLETDETECTION found in conf/modules.config and Nextflow scripts.
modules_config - SCDBLFINDER found in conf/modules.config and Nextflow scripts.
modules_config - DOUBLETREMOVAL found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_CELLCYCLE found in conf/modules.config and Nextflow scripts.
modules_config - FINALIZE_QC_ANNDATAS found in conf/modules.config and Nextflow scripts.
modules_config - QC_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - MYGENE found in conf/modules.config and Nextflow scripts.
modules_config - SET_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - HUGOUNIFIER_GET found in conf/modules.config and Nextflow scripts.
modules_config - HUGOUNIFIER_APPLY found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_UNIFY found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SUBSETVAR_INNER found in conf/modules.config and Nextflow scripts.
modules_config - SUBSETVAR_INTEGRATE found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_UPSETGENES found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_HVGS found in conf/modules.config and Nextflow scripts.
modules_config - SCRY_DEVIANCE found in conf/modules.config and Nextflow scripts.
modules_config - SCVITOOLS_SCVI found in conf/modules.config and Nextflow scripts.
modules_config - SCVITOOLS_SCANVI found in conf/modules.config and Nextflow scripts.
modules_config - SYMPHONY_HARMONYINTEGRATE found in conf/modules.config and Nextflow scripts.
modules_config - SYMPHONY_MAPEMBEDDING found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_BBKNN found in conf/modules.config and Nextflow scripts.
modules_config - SCANORAMA_INTEGRATE found in conf/modules.config and Nextflow scripts.
modules_config - SEURAT_INTEGRATION found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_COMBAT found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_PCA found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_LOG1PNORM found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_PEARSONRESIDUALS_HVGS found in conf/modules.config and Nextflow scripts.
modules_config - SCRAN_NORMALIZATION found in conf/modules.config and Nextflow scripts.
modules_config - SCARCHES_EXPIMAP found in conf/modules.config and Nextflow scripts.
modules_config - SCIMILARITY_EMBED found in conf/modules.config and Nextflow scripts.
modules_config - SCIMILARITY_ANNOTATE found in conf/modules.config and Nextflow scripts.
modules_config - SCIBMETRICS_BENCHMARK found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_MERGEEMBEDDINGS found in conf/modules.config and Nextflow scripts.
modules_config - CELLDEX_FETCHREFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - CELLTYPES_SINGLER found in conf/modules.config and Nextflow scripts.
modules_config - CELLTYPES_CELLTYPIST found in conf/modules.config and Nextflow scripts.
modules_config - CELLTYPES_AZIMUTH found in conf/modules.config and Nextflow scripts.
modules_config - CYTETYPE found in conf/modules.config and Nextflow scripts.
modules_config - NEIGHBORS found in conf/modules.config and Nextflow scripts.
modules_config - LEIDEN found in conf/modules.config and Nextflow scripts.
modules_config - ENTROPY found in conf/modules.config and Nextflow scripts.
modules_config - UMAP found in conf/modules.config and Nextflow scripts.
modules_config - TSNE found in conf/modules.config and Nextflow scripts.
modules_config - PYDESEQ2_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - EDGEPYTHON_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - EDGEPYTHON_SCDIFFERENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_PAGA found in conf/modules.config and Nextflow scripts.
modules_config - LIANA_RANKAGGREGATE found in conf/modules.config and Nextflow scripts.
modules_config - LIANA_BYSAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - CELL2CELL_TENSOR found in conf/modules.config and Nextflow scripts.
modules_config - SCANPY_RANKGENESGROUPS found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_VOLCANOPLOT found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 4.2.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.2.1
Run at 2026-10-27 19:09:23

github-actions · 2026-10-27T16:54:38Z

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

❌ modules | docker | latest-everything | Shard 2/20
❌ subworkflows | docker | latest-everything | Shard 11/12

See the full run for details.

nft-utils 1.2.1 sorts version YAML with TreeMap and casts every entry to a map. That reorders keys in existing snapshots and throws ClassCastException when a versions entry is a scalar. The pipeline tests were written against 0.0.3. Generated by Grok 4.7

nft-utils 1.2.1 sorts software-version maps, so the pipeline snapshots need to follow that order. Nest LIANA rank-aggregate versions under the process name so each entry stays a map. Generated by Grok 4.7

nf-core-bot added 3 commits July 24, 2026 12:36

Template update for nf-core/tools version 4.0.3

05dd156

Template update for nf-core/tools version 4.1.0

5f419b0

Template update for nf-core/tools version 4.2.1

98b0b82

nf-core-bot requested a review from nictru as a code owner October 26, 2026 16:05

Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…

2ee100e

…-4.2.1

nictru added 2 commits October 27, 2026 18:04

Update snapshots for nft-utils 1.2.1

8638e9a

nft-utils 1.2.1 sorts software-version maps, so the pipeline snapshots need to follow that order. Nest LIANA rank-aggregate versions under the process name so each entry stays a map. Generated by Grok 4.7

Skitionek mentioned this pull request Oct 28, 2026

feat: apply template sync PR 377 with nf-migrate #379

Closed

nictru merged commit 35b6bbc into dev Oct 28, 2026
172 of 175 checks passed

nictru deleted the nf-core-template-merge-4.2.1 branch October 28, 2026 11:03

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Important! Template update for nf-core/tools v4.2.1 - #377

Important! Template update for nf-core/tools v4.2.1#377
nictru merged 6 commits into
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nf-core-template-merge-4.2.1

nf-core-bot commented Oct 26, 2026

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github-actions Bot commented Oct 27, 2026 •

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nf-core-bot commented Oct 26, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❌ nf-test failed with latest Nextflow version

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github-actions Bot commented Oct 27, 2026 •

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

github-actions Bot commented Oct 27, 2026 •

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