Important! Template update for nf-core/tools v3.3.2 #98

nf-core-bot · 2025-07-08T11:40:35Z

Version 3.3.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.2 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 https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.3.2 release page.

mashehu · 2025-07-08T11:54:05Z

@nf-core-bot fix linting

github-actions · 2025-07-08T11:54:28Z

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

Posted for pipeline commit 5e370f9

+| ✅ 244 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  36 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config
nextflow_config - Config manifest.version should end in dev: 1.1.0
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
local_component_structure - split_id_format.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_panther_group_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - plot_orthologs.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - make_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_oma_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_inspector_group_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_eggnog_group_local.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_oma_group_local.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_panther_group_local.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - split_taxids.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - filter_fasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - filter_hits.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - make_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_oma_group_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - make_score_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_uniprot_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - identify_seq_online.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_ensembl_idmap.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - stats2csv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - make_hits_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - dump_params.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_ensembl_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - make_merge_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - write_seqinfo.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_refseq_sequences.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - get_orthologs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - score_orthologs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - merge_ids.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - report.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - get_sequences.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: docs/images/nf-core-reportho_logo_light.png

✅ 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: assets/nf-core-reportho_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/images/nf-core-reportho_logo_light.png
files_exist - File found: docs/images/nf-core-reportho_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-reportho_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/WorkflowReportho.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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 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.orthoinspector_version= Eukaryota2023
nextflow_config - Config default value correct: params.min_score= 2.0
nextflow_config - Config default value correct: params.min_identity= 90.0
nextflow_config - Config default value correct: params.min_coverage= 80.0
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/
nf_test_content - 'tests/offline.nf.test' contains outdir parameter
nf_test_content - 'tests/offline.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/offline.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/offline.nf.test' contains outdir parameter
nf_test_content - 'tests/offline.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/offline.nf.test' snapshots a 'versions.yml' file
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/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 workDir
nf_test_content - 'nf-test.config' sets a testsDir
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/branch.yml matches the template
files_unchanged - .github/workflows/linting_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 - assets/nf-core-reportho_logo_light.png matches the template
files_unchanged - docs/images/nf-core-reportho_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: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template-version-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 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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - IDENTIFY_SEQ_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_OMA_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_PANTHER_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_INSPECTOR_GROUP_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_EGGNOG_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_ID_FORMAT found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_UNIPROT_SEQUENCES found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_ENSEMBL_IDMAP found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_ENSEMBL_SEQUENCES found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_REFSEQ_SEQUENCES found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_OMA_SEQUENCES found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_HITS found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_MISSES found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_FASTA_IDS found in conf/modules.config and Nextflow scripts.
modules_config - SPLIT_TAXIDS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_FASTA_IDS found in conf/modules.config and Nextflow scripts.
modules_config - DIAMOND_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_DIAMOND found in conf/modules.config and Nextflow scripts.
modules_config - POSTPROCESS_DIAMOND found in conf/modules.config and Nextflow scripts.
modules_config - GROUP_DIAMOND found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_ALL found in conf/modules.config and Nextflow scripts.
modules_config - REDUCE_IDMAP found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_CSV found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_SCORE_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_HITS found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_ORTHOLOGS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_HITS_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_HITS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_MERGE_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - STATS2CSV found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_PARAMS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_REPORT 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
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-07-08 13:37:16

nf-core-bot and others added 2 commits July 8, 2025 11:39

Template update for nf-core/tools version 3.3.2

70cb955

Merge branch 'dev' into nf-core-template-merge-3.3.2

ce13c17

[automated] Fix code linting

38c7a25

itrujnara added 2 commits July 8, 2025 14:35

Make linter happy

45b0ad9

Update snapshots after multiqc update

5e370f9

mashehu approved these changes Jul 8, 2025

View reviewed changes

itrujnara merged commit 26170ae into dev Jul 8, 2025
14 checks passed

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Uh oh!

Important! Template update for nf-core/tools v3.3.2 #98

Important! Template update for nf-core/tools v3.3.2 #98

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nf-core-bot commented Jul 8, 2025

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mashehu commented Jul 8, 2025

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github-actions bot commented Jul 8, 2025 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Important! Template update for nf-core/tools v3.3.2 #98

Important! Template update for nf-core/tools v3.3.2 #98

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mashehu commented Jul 8, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented Jul 8, 2025 •

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