Dev by PelzKo · Pull Request #3 · daisybio/domainsplit

PelzKo · 2026-06-12T10:54:11Z

PR checklist

New datasets

github-actions · 2026-06-12T10:55:52Z

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

Posted for pipeline commit dfb8697

+| ✅ 182 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   4 tests failed       |-

Details

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 1.0.0dev
version_consistency - manifest.version was not numeric: 1.0.0dev!
version_consistency - nfcore_yml.version was not numeric: 1.0.0dev!
included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/domainsplit/domainsplit/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-domainsplit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-domainsplit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-domainsplit_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-domainsplit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-domainsplit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-domainsplit_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/domainsplit/domainsplit/.github/workflows/awstest.yml
multiqc_config - multiqc_config

✅ 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: 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/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: 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/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: conf/base.config
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-domainsplit_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/WorkflowDomainsplit.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 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.url_3did= https://3did.irbbarcelona.org/download/current/3did.sql.gz
nextflow_config - Config default value correct: params.url_uniprot_id_mapping= https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz
nextflow_config - Config default value correct: params.url_uniprot_prott5_embeddings= https://ftp.ebi.ac.uk/pub/contrib/UniProt/embeddings/current_release/UP000005640_9606/per-residue.h5
nextflow_config - Config default value correct: params.url_uniprot_go_terms= https://rest.uniprot.org/uniprotkb/stream?compressed=true&fields=accession%2Cgo_id&format=tsv&query=%28%28database%3AGO%29+AND+%28reviewed%3Atrue%29%29
nextflow_config - Config default value correct: params.url_uniprot_sequences= https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
nextflow_config - Config default value correct: params.url_negatome= https://mips.helmholtz-muenchen.de/proj/ppi/negatome/combined_pfam.txt
nextflow_config - Config default value correct: params.url_string= https://stringdb-downloads.org/download/protein.links.v12.0/9606.protein.links.v12.0.txt.gz
nextflow_config - Config default value correct: params.url_pfam2go= https://current.geneontology.org/ontology/external2go/pfam2go
nextflow_config - Config default value correct: params.url_pfam_template= https://www.ebi.ac.uk/interpro/wwwapi//entry/pfam/{pfam_id}/?annotation=alignment:full&download
nextflow_config - Config default value correct: params.esm_protein_shards= 4
nextflow_config - Config default value correct: params.esm_domain_shards= 1
nextflow_config - Config default value correct: params.esm_batch_size_protein= 8
nextflow_config - Config default value correct: params.esm_batch_size_domain= 32
nextflow_config - Config default value correct: params.esm_max_len= 4096
nextflow_config - Config default value correct: params.esm_smoke_test= false
nextflow_config - Config default value correct: params.negative_ppi_min_n_tested= 5
nextflow_config - Config default value correct: params.negative_ppi_seed= 42
nextflow_config - Config default value correct: params.pfam_download_batch_size= 100
nextflow_config - Config default value correct: params.url_uniprot_swissprot_pfam= https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=tsv&fields=accession%2Cid%2Cgene_names%2Cxref_pfam&query=%28%28reviewed%3Atrue%29+AND+%28organism_id%3A9606%29%29
nextflow_config - Config default value correct: params.hippie_min_score= 0.63
nextflow_config - Config default value correct: params.ppidm_classes= Bronze,Silver,Gold
nextflow_config - Config default value correct: params.self_interaction= true
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.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/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 - LICENSE matches the template
files_unchanged - .github/.dockstore.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
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
readme - README Nextflow minimum version badge matched config. Badge: 25.10.2, Config: 25.10.2
readme - README nf-core template version badge found.
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: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.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: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
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 - MMSEQS_EASYCLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - INIT_DOMAINSPLIT_DB found in conf/modules.config and Nextflow scripts.
modules_config - INSERT_PPI_NEGATIVE_SELECTION found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_UNIQUE_DOMAINS 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.
version_consistency - Version tags are consistent: manifest.version = 1.0.0dev, nfcore_yml.version = 1.0.0dev

Run details

nf-core/tools version 4.0.2
Run at 2026-06-12 10:55:33

PelzKo and others added 17 commits June 9, 2026 18:30

added two more positive sources

46e16a5

updated mmseqs, made the negative sampling use dans

36b05f6

fixed warnings

33b5894

changed something back written by claude

d9575d3

fixed errors

b790ec8

changed two parameters for prott5 into one

9a4832c

tried new improved method for sampling negative data

c37ab02

reworked generating negatives

097bd3b

updated schema

6be7b1a

dont add nf-test to github

77df26d

marked required files as required, fixed json in test

64f915b

updated tests

bc681c5

removed docker:// prefix for containers

3450738

fixed docker prefix

a40248a

added docker home directory

2aca8c5

removed stuff from snapshot

a09986f

Merge pull request #2 from daisybio/new_datasets

dfb8697

New datasets

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PelzKo wants to merge 17 commits into
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PelzKo commented Jun 12, 2026

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github-actions Bot commented Jun 12, 2026

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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PelzKo commented Jun 12, 2026

PR checklist

Uh oh!

github-actions Bot commented Jun 12, 2026

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

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