Template updates, nf-test and more #382

erikrikarddaniel · 2025-06-16T12:48:17Z

PR checklist

Template updates: 3.2.1 and 3.3.1
Pipeline nf-tests
Various smaller improvements.

Post release version bump

improved readability

…ngelog

Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>

Fix/trimlogs undefined error

fix: Correct Transdecoder publishing and test assertions

Deal with duplicates in NCBI taxonomy

bioconda's version is superseded by conda-forge's wget; nf-core should use it - and so be able to pick up the aarch64 support.

Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>

Update environment.yml: use wget not gnu-wget

Fix broken tests

Version bump

github-actions · 2025-06-16T12:50:12Z

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

Posted for pipeline commit 90d50f0

+| ✅ 265 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/nf-core-metatdenovo_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-metatdenovo_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-metatdenovo_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-metatdenovo_logo_light.png
files_exist - File found: docs/images/nf-core-metatdenovo_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: conf/igenomes_ignored.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-metatdenovo_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/WorkflowMetatdenovo.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 manifest.version does not contain dev for release: 1.2.0
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.bbnorm_target= 100
nextflow_config - Config default value correct: params.bbnorm_min= 5
nextflow_config - Config default value correct: params.user_assembly_name= user_assembly
nextflow_config - Config default value correct: params.min_contig_length= 0
nextflow_config - Config default value correct: params.spades_flavor= rna
nextflow_config - Config default value correct: params.bbmap_minid= 0.9
nextflow_config - Config default value correct: params.user_orfs_name= user_orfs
nextflow_config - Config default value correct: params.prokka_batchsize= 10 MB
nextflow_config - Config default value correct: params.eggnog_dbpath= eggnog
nextflow_config - Config default value correct: params.kofam_dir= ./kofam/
nextflow_config - Config default value correct: params.hmmpattern= *.hmm
nextflow_config - Config default value correct: params.diamond_top= 10
nextflow_config - Config default value correct: params.eukulele_method= mets
nextflow_config - Config default value correct: params.eukulele_dbpath= ./eukulele/
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/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/megahit_transdecoder.nf.test' contains outdir parameter
nf_test_content - 'tests/megahit_transdecoder.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/megahit_transdecoder.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/megahit_prokka.nf.test' contains outdir parameter
nf_test_content - 'tests/megahit_prokka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/megahit_prokka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spades_prodigal.nf.test' contains outdir parameter
nf_test_content - 'tests/spades_prodigal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spades_prodigal.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 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/CONTRIBUTING.md 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 - docs/images/nf-core-metatdenovo_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_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: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_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: awstest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.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 - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_MERGEPE found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBNORM found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
modules_config - MEGAHIT_INTERLEAVED found in conf/modules.config and Nextflow scripts.
modules_config - WRITESPADESYAML found in conf/modules.config and Nextflow scripts.
modules_config - SPADES found in conf/modules.config and Nextflow scripts.
modules_config - FORMATSPADES found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SEQ_CONTIG_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - PRODIGAL found in conf/modules.config and Nextflow scripts.
modules_config - FORMAT_PRODIGAL_GFF found in conf/modules.config and Nextflow scripts.
modules_config - TRANSDECODER found in conf/modules.config and Nextflow scripts.
modules_config - PIGZ_TRANSDECODER_ found in conf/modules.config and Nextflow scripts.
modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - FAA_CAT found in conf/modules.config and Nextflow scripts.
modules_config - FFN_CAT found in conf/modules.config and Nextflow scripts.
modules_config - GFF_CAT found in conf/modules.config and Nextflow scripts.
modules_config - PROKKAGFF2TSV found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_HMMHITFAAS found in conf/modules.config and Nextflow scripts.
modules_config - HMMRANK found in conf/modules.config and Nextflow scripts.
modules_config - EGGNOG_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - EGGNOG_MAPPER found in conf/modules.config and Nextflow scripts.
modules_config - KOFAMSCAN_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - KOFAMSCAN_SCAN found in conf/modules.config and Nextflow scripts.
modules_config - KOFAMSCAN_UNIQUE found in conf/modules.config and Nextflow scripts.
modules_config - EUKULELE_SEARCH found in conf/modules.config and Nextflow scripts.
modules_config - DIAMOND_TAXONOMY found in conf/modules.config and Nextflow scripts.
modules_config - TAXONKIT_LINEAGE found in conf/modules.config and Nextflow scripts.
modules_config - PIGZ_DIAMOND_LINEAGE found in conf/modules.config and Nextflow scripts.
modules_config - FORMAT_DIAMOND_TAX_RANKLIST found in conf/modules.config and Nextflow scripts.
modules_config - FORMAT_DIAMOND_TAX_TAXDUMP found in conf/modules.config and Nextflow scripts.
modules_config - FORMAT_EUKULELE_TAX found in conf/modules.config and Nextflow scripts.
modules_config - SUM_EUKULELE_TAXONOMY found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_STATS found in conf/modules.config and Nextflow scripts.
modules_config - TRANSRATE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.3.1
Run at 2025-06-18 05:29:32

Package versions are not synced between Conda and containers, and there are conflicts I can't currently resolve.

.nf-core.yml

modules/local/kofamscan/unique/tests/main.nf.test

conf/igenomes.config

workflows/metatdenovo.nf

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

Remove test for kofamscan/unique

danilodileo

LGTM!

erikrikarddaniel and others added 30 commits January 21, 2025 14:15

Template update for nf-core/tools version 3.1.2

58ed656

Bump version to 1.1.2

7ea760d

Merge pull request #356 from erikrikarddaniel/bump-versions

4917055

Post release version bump

improved readability

7452b91

link to the PR updated in changelog

096cd2b

removing duplicated lines

21ad70f

Merge pull request #359 from herich0/json-schema-improvements

85d72d6

improved readability

Fix undefined read_trimlogs error when trimlogs is false + test + cha…

5530c4c

…ngelog

Update CHANGELOG.md

db91496

Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>

Update CHANGELOG.md

cbbae24

Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>

Update CHANGELOG.md

55d66cf

lint: final newline char

3dbe172

Merge pull request #361 from m3hdad/fix/trimlogs-undefined-err

89edcb9

Fix/trimlogs undefined error

fix: Correct Transdecoder publishing and update test

f1ffae8

Changelog update

f818425

Merge pull request #362 from m3hdad/fix/transdecoder-publishDir

8a8291c

fix: Correct Transdecoder publishing and test assertions

Try to deal with duplicates in NCBI taxonomy

2b98070

CHANGELOG.md

112780f

Spelling mistake

141d5c5

Small update to CHANGELOG.md

91661a4

Another writing mistake

ccf61dc

Merge pull request #363 from erikrikarddaniel/fix-ncbi-taxonomy-parsing

ca86300

Deal with duplicates in NCBI taxonomy

(str) add eukulele database name to output dir if exists

a818250

Update environment.yml: use wget not gnu-wget

55354ba

bioconda's version is superseded by conda-forge's wget; nf-core should use it - and so be able to pick up the aarch64 support.

Update CHANGELOG.md

db07d72

Update CHANGELOG.md: is this why lint doesn't like me today?

1ef3975

Update CHANGELOG.md

bf33898

Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>

chore: Bump containers

36ba1b4

Update CHANGELOG.md

02cbd7c

Merge pull request #364 from nf-core/dslarm-patch-1

4744734

Update environment.yml: use wget not gnu-wget

erikrikarddaniel added 13 commits June 16, 2025 09:44

Improve module version handling

f164bc6

Merge branch 'more-nf-tests' into dev

96010d9

Bump version

039d9ba

Update CHANGELOG.md

5140378

Revert version bump

b4549ab

Update snapshots

c0eef98

Fix mistake in version bump reversion

33f0110

Update snapshots

a438eaa

Update CHANGELOG.md

41309f8

ignore also spades.yaml

c9be42f

Merge pull request #380 from erikrikarddaniel/fix-broken-tests

974329a

Fix broken tests

Version bump

56ea47e

Merge pull request #381 from erikrikarddaniel/dev

7b42bf7

Version bump

Disable conda tests

cd51228

Package versions are not synced between Conda and containers, and there are conflicts I can't currently resolve.

maxulysse reviewed Jun 17, 2025

View reviewed changes

.nf-core.yml Outdated Show resolved Hide resolved

maxulysse reviewed Jun 17, 2025

View reviewed changes

modules/local/kofamscan/unique/tests/main.nf.test Outdated Show resolved Hide resolved

maxulysse reviewed Jun 17, 2025

View reviewed changes

conf/igenomes.config Outdated Show resolved Hide resolved

maxulysse reviewed Jun 17, 2025

View reviewed changes

workflows/metatdenovo.nf Outdated Show resolved Hide resolved

erikrikarddaniel and others added 4 commits June 17, 2025 09:56

Update .nf-core.yml

c3ea523

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

Update workflows/metatdenovo.nf

3343a3a

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>

Remove test for kofamscan/unique

43a3e85

Merge pull request #384 from erikrikarddaniel/dev

ac07d9e

Remove test for kofamscan/unique

maxulysse approved these changes Jun 17, 2025

View reviewed changes

Update version and date in CHANGELOG.md

193f26e

erikrikarddaniel requested review from danilodileo June 17, 2025 10:50

danilodileo approved these changes Jun 17, 2025

View reviewed changes

Update CHANGELOG.md

90d50f0

erikrikarddaniel merged commit c58c01c into master Jun 18, 2025
25 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Template updates, nf-test and more #382

Template updates, nf-test and more #382

Uh oh!

Uh oh!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Template updates, nf-test and more #382

Template updates, nf-test and more #382

Uh oh!

Conversation

Uh oh!

PR checklist

Uh oh!

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

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