Added functional meta.yml and test by Muskan-2464 · Pull Request #91 · nf-core/proteinannotator

Muskan-2464 · 2026-03-13T17:33:59Z

PR checklist

nf-core-bot · 2026-03-13T17:34:39Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

vagkaratzas

Left comments to revise. In addition:

when staging files, and before commiting them, run pre-commit locally so formatting issues are tackled there
make sure nf-core subworkflows lint command passes all test for this subworkflow
Run the nf-test test /path/to/test/main.nf.test --profile +singularity --verbose command twice; one to generate the snapshot, and then once more to make sure the snapshot is not changing.

github-actions · 2026-03-28T14:01:33Z

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

Posted for pipeline commit 38be11c

+| ✅ 218 tests passed       |+
#| ❔   7 tests were ignored |#

Details

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-proteinannotator_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_dark.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-proteinannotator_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-proteinannotator_logo_light.png
files_exist - File found: docs/images/nf-core-proteinannotator_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-proteinannotator_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/WorkflowProteinannotator.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.1.0dev
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.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/
nextflow_config - Config default value correct: params.min_seq_length= 30
nextflow_config - Config default value correct: params.max_seq_length= 5000
nextflow_config - Config default value correct: params.pfam_latest_link= https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
nextflow_config - Config default value correct: params.funfam_latest_link= https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz
nextflow_config - Config default value correct: params.nmpfams_latest_link= https://pavlopoulos-lab.org/envofams/databases/hmmer/nmpfamsdb.hmm.gz
nextflow_config - Config default value correct: params.hmmsearch_evalue_cutoff= 0.001
nextflow_config - Config default value correct: params.skip_interproscan= false
nextflow_config - Config default value correct: params.interproscan_db_url= https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz
nextflow_config - Config default value correct: params.interproscan_applications= Hamap,PANTHER,PIRSF,TIGRFAM,sfld
nextflow_config - Config default value correct: params.s4pred_outfmt= ss2
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 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/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/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: 25.10.0, Config: 25.10.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.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 - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_PROTEINANNOTATOR 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-30 07:55:59

vagkaratzas

Good job, thank you @Muskan-2464 :D
I made a small tweak to the input file of the main test, and also added a needed config, otherwise INTERPROSCAN would not properly execute on the GitHub runner.

Muskan-2464 added 21 commits March 13, 2026 16:11

Create main.nf.test

3787af6

Create meta.yml

e5cb774

nextflow.config

c454590

main.nf.test.snap

300d7db

main.nf.test

c077dc6

meta.yml

0f1090e

main.nf.test

e5c1c4d

meta.yml

c502cc4

main.nf.test

59e5524

meta.yml

fb9b08f

main.nf.test

83d283b

Delete subworkflows/local/functional_annotation/tests/main.nf.test.snap

2addcae

Delete subworkflows/local/functional_annotation/tests/nextflow.config

ae64892

meta.yml

b28f4ac

main.nf.test

9a4eb92

main.nf.test

0af79b7

main.nf.test

22b90c8

main.nf.test

4b78ba7

main.nf.test

672c597

main.nf.test

43ac518

Add snapshot for functional_annotation

a8e313d

Muskan-2464 added 4 commits March 13, 2026 23:16

meta.yml

b9cf9a3

meta.yml

e9105dc

meta.yml

adbae43

Fix trailing whitespace in meta.yml

95c9f0c

Muskan-2464 marked this pull request as ready for review March 13, 2026 18:52

vagkaratzas requested changes Mar 20, 2026

View reviewed changes

vagkaratzas reviewed Mar 20, 2026

View reviewed changes

Comment thread subworkflows/local/functional_annotation/tests/main.nf.test Outdated

fixed the suggested change

c14ad9e

Muskan-2464 and others added 5 commits March 28, 2026 14:21

Fix syntax error in main.nf.test

d84dc5d

updated suggested code

a7ad7b7

completed suggested changes

23bb6d8

fixed input paths

ec80026

update meta.yml descriptions and fix failing test

38be11c

vagkaratzas self-requested a review March 30, 2026 07:56

vagkaratzas approved these changes Mar 30, 2026

View reviewed changes

vagkaratzas merged commit e4da269 into dev Mar 30, 2026
12 checks passed

vagkaratzas deleted the add-functional-meta-and-test-2 branch March 30, 2026 07:59

vagkaratzas mentioned this pull request Mar 30, 2026

Add nf-test and meta.yml files for the local functional_annotation subworkflow #78

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Added functional meta.yml and test #91

Added functional meta.yml and test #91
vagkaratzas merged 31 commits into
devfrom
add-functional-meta-and-test-2

Muskan-2464 commented Mar 13, 2026

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github-actions Bot commented Mar 28, 2026 •

edited

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❔ Tests ignored:

✅ Tests passed:

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Muskan-2464 commented Mar 13, 2026

PR checklist

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github-actions Bot commented Mar 28, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions Bot commented Mar 28, 2026 •

edited

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