Issue 77 by npechl · Pull Request #87 · nf-core/proteinannotator

npechl · 2026-03-12T13:45:27Z

PR checklist

Fixes #77.

First pipeline release

zenodo updated

nf-core-bot · 2026-03-12T13:46:02Z

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.

github-actions · 2026-03-12T14:22:30Z

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

Posted for pipeline commit 70a7ba3

+| ✅ 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: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.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: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_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'
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 2026-03-14 10:15:52

vagkaratzas

Nice one! Maybe change the names of the existing tests (let them test what they already do), and just add an extra test that runs only nmpfams. Can you please also revert the paths that I mentioned in the PR? remember to --update-snapshot, and all tests should pass OK!

nextflow_schema.json

subworkflows/local/domain_annotation/main.nf

subworkflows/local/domain_annotation/tests/main.nf.test

conf/test_full.config

conf/test.config

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

vagkaratzas

LGTM!

vagkaratzas and others added 11 commits February 9, 2026 12:48

Merge pull request #71 from nf-core/dev

382d936

First pipeline release

zenodo updated

88107cd

Merge pull request #76 from nf-core/zenodo-update-main

381c431

zenodo updated

first commit

60b847d

update configs

bec80f6

update utils

18d9b16

fix link

7dc19a6

update domain_annotation meta

3a50b21

update main workflow

80758f5

fix typos

acef4be

include testing

f70acaa

npechl and others added 2 commits March 12, 2026 13:57

fix naming

21e5436

Merge branch 'dev' into issue_77

392021e

npechl added 9 commits March 12, 2026 14:43

fix naming

01310a0

fix testing

185ce5a

fix typo

9a6bc83

fix typo

c88e6c4

update testdata link

585808d

update testddata path

023f0ca

update snap

9908739

update docs

c6b401e

update changelog & readme

c1ec64e

npechl marked this pull request as ready for review March 13, 2026 11:34

vagkaratzas requested changes Mar 13, 2026

View reviewed changes

npechl and others added 4 commits March 13, 2026 14:05

Update subworkflows/local/domain_annotation/main.nf

61028d8

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

revert links

73fa894

revision

7c30cdf

spaces

e9ad2c6

npechl and others added 5 commits March 13, 2026 14:54

include nmpfams test

1f920fe

fix spacing

242ff95

update test config

9f0e6fb

update nftignore

22c27fb

module configs updated for nmpfams, end-to-end test snapshot updated

70a7ba3

vagkaratzas self-requested a review March 14, 2026 10:21

vagkaratzas approved these changes Mar 14, 2026

View reviewed changes

vagkaratzas merged commit 68c1d7e into dev Mar 14, 2026
17 checks passed

vagkaratzas deleted the issue_77 branch March 14, 2026 10:21

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Issue 77#87

Issue 77#87
vagkaratzas merged 31 commits intodevfrom
issue_77

npechl commented Mar 12, 2026 •

edited

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edited

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❔ Tests ignored:

✅ Tests passed:

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npechl commented Mar 12, 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:

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npechl commented Mar 12, 2026 •

edited

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github-actions bot commented Mar 12, 2026 •

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