First pipeline release by vagkaratzas · Pull Request #71 · nf-core/proteinannotator

vagkaratzas · 2026-02-04T13:15:26Z

v1.0.0 - Yellow Saiga - [2026/02/04]

Initial release of nf-core/proteinannotator, created with the nf-core template.

#68 - Using the ARIA2 and UNTAR nf-core modules to download and decompress the InterProScan database. (by @vagkaratzas)
#67 - Swapped to the updated, non-buggy, nf-core version of INTERPROSCAN. (by @vagkaratzas)
#65 - Converted the pipeline schematic to nf-core metromap. (by @vagkaratzas)
#62 - Added the option to download and use the latest FunFam HMM library (or use path to an existing one) for domain annotation. (by @vagkaratzas)
#61 - Added nf-core modules ARIA2 and HMMER_HMMSEARCH to download latest Pfam HMM library (or use path to existing one) and match domains to input sequences. (by @vagkaratzas)
#60 - Added nf-core module S4PRED_RUNMODEL for secondary structure prediction (i.e., α-helix, a β-strand or a coil). (by @vagkaratzas)
#59 - Added nf-core qc and pre-processing subworkflow for amino acid sequences FAA_SEQFU_SEQKIT. (by @vagkaratzas)
#57 - nf-core tools template update to 3.5.1. (by @vagkaratzas)
#52 - Add option to turn off InterProScan for testing. (by @edmundmiller, @olgabot)
#51 - Update to nf-core/tools v3.3.1. (by @olgabot)
#47 - Update metromap with more tools added from May 2025 Hackathon. (by @olgabot)
#42 - Updated to nf-test on GitHub Actions and in the PULL_REQUEST_TEMPLATE.md. (by @olgabot)
#13 - Add nf-core seqkit/stats module. (by @olgabot, @heuermh)
#9 - Added InterProScan module - local version. (by @olgabot, @heuermh, @eweizy)

PR checklist

…rties file during interproscan run

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

Ips db aria2

Use nf-core interproscan instead of local version

pipeline description and nf-core modules updates

version bump + fix release lint + github handles for credits

nf-core-bot · 2026-02-04T13:15:58Z

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 · 2026-02-04T13:17:09Z

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

Posted for pipeline commit bf1bee7

+| ✅ 213 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ 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 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.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.
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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_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: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.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 - 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-02-09 12:27:10

nschan

Here is my review! Overall, this looks like a nice pipeline to me

vagkaratzas · 2026-02-04T16:29:47Z

Addressing @nschan's points through this PR #72

release-review-points

jfy133

Beautiful well done @vagkaratzas @olgabot and team!

Just need to work out why your full test is not triggering, then you're good to merge!

…d db for reuse

second reviewer comments resolve

olgabot and others added 30 commits April 21, 2025 18:04

Trying to figure out the untar thing

f595b15

Add excalidraw version of metromap

a3b6e7f

Add metromap to readme

30831e4

Testing local scripts with interproscan setup

9221909

Remove interproscan setup in favor of updating the interproscan.prope…

b8d6287

…rties file during interproscan run

Update snapshot, change interproscan properties

f63278e

Now testing full interproscan subworkflow

3f3ba95

Remove interproscan setup py file

9f44f9b

Remove call to interproscan setup

0c85d74

Interproscan workflow tests seem to work

60097d4

rename nf-test CI to be more explicit

d773779

try using setup-nf-test

15d330c

Try adding jobs: and tests

8f290bf

try nf-test action from nf-core/modules

accbefd

Try a frankenversion of the github actions

121a41f

Always use singularity

7214c11

Add environment variables

b1bc8d8

Remove nft environment variables

91db590

remove filter

c5b571b

Remove the nf environment variables altogether

d8650ea

Remove slash after --ci

e2f4288

Update nf test config to use base directory for finding tests

72bb310

Ignore autogenerated nf-test files

8b79972

Add test summary to CI output

fd6fbd8

Only run nf-test on interproscan for now

78c6629

--tags -> --tag (singular)

9489ea3

Add "test" profile for nf-test

a6298c5

Template update for nf-core/tools version 3.2.1

b09cd0c

Merge branch 'dev' into nf-core-template-merge-3.2.1

1ce3f1f

Fix lint errors due to merge

aa2e68b

vagkaratzas and others added 16 commits February 2, 2026 15:05

unused untar module removed, end-to-end snapshot updated

920faca

output.md updated

9330e1e

snapshot updated

2499059

Update docs/usage.md

b602514

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

fix identation

f8a95ad

removed test-related line from output.md

f8fdee9

aria2 and untar for ips db

9c476b2

changelog update

0cb0ad2

.first() added

a407f49

Merge pull request #68 from nf-core/ips-db-aria2

22f5e2f

Ips db aria2

Merge pull request #67 from nf-core/nf-core-interproscan

b4af633

Use nf-core interproscan instead of local version

pipeline descr change

2ff19cd

module updates

a4d3fe5

Merge pull request #69 from nf-core/pre-release-small-updates

d0eeb5e

pipeline description and nf-core modules updates

version bump + fix release lint + github handles for credits

325a549

Merge pull request #70 from vagkaratzas/dev

3295bde

version bump + fix release lint + github handles for credits

nschan reviewed Feb 4, 2026

View reviewed changes

release-review-points

e495e62

Merge pull request #72 from vagkaratzas/dev

26f4d3d

release-review-points

vagkaratzas requested a review from nschan February 5, 2026 11:03

nschan approved these changes Feb 5, 2026

View reviewed changes

jfy133 approved these changes Feb 9, 2026

View reviewed changes

vagkaratzas and others added 4 commits February 9, 2026 09:55

second reviewer comments resolve

f76cb33

pipeline description updated

b9661af

sentence added on usage.md, suggesting to keep interproscan downloade…

903d955

…d db for reuse

Merge pull request #74 from vagkaratzas/changes-second-review

bf1bee7

second reviewer comments resolve

vagkaratzas merged commit 382d936 into main Feb 9, 2026
36 checks passed

Conversation

vagkaratzas commented Feb 4, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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v1.0.0 - Yellow Saiga - [2026/02/04]

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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vagkaratzas commented Feb 4, 2026

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vagkaratzas commented Feb 4, 2026 •

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github-actions Bot commented Feb 4, 2026 •

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