Update m s by vagkaratzas · Pull Request #95 · nf-core/proteinannotator

vagkaratzas · 2026-05-05T10:19:39Z

PR checklist

post-release version bump

… to nextflow.config

…duction full test correct input samplesheet path, typos fix, zenodo doi added…

…root tar file?

Added functional meta.yml and test

Add metagroot domain annot

Important! Template update for nf-core/tools v4.0.2

github-actions · 2026-05-05T10:19:49Z

This PR is against the `main` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @vagkaratzas,

It looks like this pull-request is has been made against the nf-core/proteinannotator main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the nf-core/proteinannotator dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2026-05-05T10:21:38Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 3b2b74e

+| ✅ 228 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   3 tests failed       |-

Details

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 1.1.0dev
version_consistency - manifest.version was not numeric: 1.1.0dev!
version_consistency - nfcore_yml.version was not numeric: 1.1.0dev!

❗ Test warnings:

pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/proteinannotator/proteinannotator/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_

❔ 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/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/CONTRIBUTING.md
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 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.metagroot_latest_link= https://pavlopoulos-lab.org/envofams/databases/hmmer/metagroot.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/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: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO 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: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awstest.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 - 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: 4.0.2
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
version_consistency - Version tags are consistent: manifest.version = 1.1.0dev, nfcore_yml.version = 1.1.0dev
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 4.0.2
Run at 2026-05-05 10:21:22

vagkaratzas and others added 30 commits February 9, 2026 14:05

post-release version bump

a1a8346

Merge pull request #75 from vagkaratzas/dev

f02fbba

post-release version bump

first commit

60b847d

update configs

bec80f6

update utils

18d9b16

fix link

7dc19a6

update domain_annotation meta

3a50b21

update main workflow

80758f5

fix typos

acef4be

full test correct input samplesheet path, typos fix, zenodo doi added…

b8f62f1

… to nextflow.config

Merge pull request #85 from nf-core/minor-fixes-typos-and-usage-intro…

5a7b85b

…duction full test correct input samplesheet path, typos fix, zenodo doi added…

include testing

f70acaa

fix naming

21e5436

Merge branch 'dev' into issue_77

392021e

fix naming

01310a0

fix testing

185ce5a

fix typo

9a6bc83

fix typo

c88e6c4

copying integration of pfam and funfam

2ad495f

nf-core modules wget and untar as a workaround for aria2 to get metag…

63fd565

…root tar file?

update testdata link

585808d

update testddata path

023f0ca

update snap

9908739

update docs

c6b401e

update changelog & readme

c1ec64e

Create main.nf.test

3787af6

Create meta.yml

e5cb774

nextflow.config

c454590

main.nf.test.snap

300d7db

main.nf.test

c077dc6

Muskan-2464 and others added 27 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

Merge pull request #91 from nf-core/add-functional-meta-and-test-2

e4da269

Added functional meta.yml and test

Merge branch 'dev' into add-metagroot-domain-annot

0c42195

fix ARIA2_MROOT and take: alignment

6943064

replace 'mroot' with 'metagroot'

1cf0555

align = and comments

f137226

remove nf-core/module wget

a06b808

add MetagRoot to docs

35c56e9

align =

38d2c48

update snapshot for domain_annotation tests

6a539e9

updated meta via nf-core pipelines lint

7f8269b

add missing skip param

406b4cf

rename metagrootdb_test to metagroot_test

0ecbfdf

pipeline-level snapshot updated

60f38c7

rename MetagRoot to metagRoot

972f149

Merge pull request #90 from nf-core/add-metagroot-domain-annot

96885a2

Add metagroot domain annot

Template update for nf-core/tools version 4.0.0

d770b6b

Template update for nf-core/tools version 4.0.2

5cabc5a

Merge branch 'dev' into nf-core-template-merge-4.0.2

7c36646

ro-crate lint

cc0cab2

monochrome logs and prek all files fix

863ba7d

Merge pull request #93 from nf-core/nf-core-template-merge-4.0.2

8942468

Important! Template update for nf-core/tools v4.0.2

update nf-core modules and subworkflows to latest

3b2b74e

vagkaratzas closed this May 5, 2026

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Update m s#95

Update m s#95
vagkaratzas wants to merge 88 commits into
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vagkaratzas commented May 5, 2026

Uh oh!

github-actions Bot commented May 5, 2026

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github-actions Bot commented May 5, 2026 •

edited

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vagkaratzas commented May 5, 2026

PR checklist

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github-actions Bot commented May 5, 2026

This PR is against the main branch ❌

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github-actions Bot commented May 5, 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: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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This PR is against the `main` branch ❌

github-actions Bot commented May 5, 2026 •

edited

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`nf-core pipelines lint` overall result: Failed ❌