Fix release lints from template 3.3.1 #95

itrujnara · 2025-06-17T12:50:29Z

This PR fixes lint issues that appeared in the release PR after updating the template

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
Make sure your code lints (nf-core lint).

This fixes the download test in CI

github-actions · 2025-06-17T12:52:13Z

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

Posted for pipeline commit c06a94a

+| ✅ 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: 24.04.2, Config: 24.04.2
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: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.1
Run at 2025-06-17 14:54:09

itrujnara added 3 commits June 17, 2025 14:29

Enable custom configs

4d8afe8

Replace mulled containers with Seqera Containers

4d5aab9

This fixes the download test in CI

Update DIAMOND/CLUSTER module

e56ecce

itrujnara added 2 commits June 17, 2025 15:18

Update DIAMOND/CLUSTER again

ef1373b

Fix nf-test config to skip testing nf-core modules

04a3397

mashehu approved these changes Jun 17, 2025

View reviewed changes

Update test snapshot after module update

c06a94a

itrujnara merged commit 017db56 into nf-core:dev Jun 17, 2025
13 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Fix release lints from template 3.3.1 #95

Fix release lints from template 3.3.1 #95

Uh oh!

itrujnara commented Jun 17, 2025

Uh oh!

github-actions bot commented Jun 17, 2025 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Fix release lints from template 3.3.1 #95

Fix release lints from template 3.3.1 #95

Uh oh!

Conversation

itrujnara commented Jun 17, 2025

PR checklist

Uh oh!

github-actions bot commented Jun 17, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

github-actions bot commented Jun 17, 2025 •

edited

Loading

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