Extending db options by brovolia · Pull Request #22 · nf-core/bacmodel

brovolia · 2026-07-30T11:24:34Z

Addressing the comments in the right branch

Points every test_*.config at the samplesheet.tsv hosted on nf-core/test-datasets (bacmodel branch) instead of the local assets/samplesheet.csv, matching test_full.config and the usual nf-core convention of keeping CI test inputs in the test-datasets repo. Requires the companion test-datasets PR that adds the optional medium_* columns to samplesheet.tsv, so test_carveme.config keeps exercising the gap-filling-on-a-medium code path.

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# Conflicts: # .nf-core.yml

github-actions · 2026-07-30T11:25:20Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-07-30T11:26:06Z

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

Posted for pipeline commit 3010441

+| ✅ 210 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   6 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).
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in environment.yml: List required Conda package(s).

❔ 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: .github/workflows/linting_comment.yml
nextflow_config - Config default ignored: params.baktadb
nextflow_config - Config default ignored: params.pfamdb
nextflow_config - Config default ignored: params.macsyfinder_db
files_unchanged - files_unchanged
template_strings - template_strings
multiqc_config - multiqc_config
container_configs - container_configs

✅ 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.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-bacmodel_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-bacmodel_logo_light.png
files_exist - File found: docs/images/nf-core-bacmodel_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: 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-bacmodel_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/WorkflowBacmodel.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.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.annotation_tool= prokka
nextflow_config - Config default value correct: params.baktadb_type= light
nextflow_config - Config default value correct: params.min_contig_length= 200
nextflow_config - Config default value correct: params.skip_macsyfinder= false
nextflow_config - Config default value correct: params.macsyfinder_models= TXSS
nextflow_config - Config default value correct: params.macsyfinder_db_type= unordered
nextflow_config - Config default value correct: params.skip_traitar= false
nextflow_config - Config default value correct: params.skip_carveme= false
nextflow_config - Config default value correct: params.skip_gapseq= true
nextflow_config - Config default value correct: params.skip_memote= true
nf_test_content - 'tests/gapseq.nf.test' contains outdir parameter
nf_test_content - 'tests/gapseq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/gapseq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/traitar.nf.test' contains outdir parameter
nf_test_content - 'tests/traitar.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/traitar.nf.test' snapshots a 'versions.yml' file
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/gapseq_custom.nf.test' contains outdir parameter
nf_test_content - 'tests/gapseq_custom.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/gapseq_custom.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bakta.nf.test' contains outdir parameter
nf_test_content - 'tests/bakta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bakta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/carveme.nf.test' contains outdir parameter
nf_test_content - 'tests/carveme.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/carveme.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/full.nf.test' contains outdir parameter
nf_test_content - 'tests/full.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/full.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/macsyfinder.nf.test' contains outdir parameter
nf_test_content - 'tests/macsyfinder.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/macsyfinder.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
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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge 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
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: pr-comment.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: 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 - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTADBDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - MACSYFINDER_SEARCH found in conf/modules.config and Nextflow scripts.
modules_config - MACSYFINDER_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - TRAITAR found in conf/modules.config and Nextflow scripts.
modules_config - TRAITAR_PFAMGET found in conf/modules.config and Nextflow scripts.
modules_config - CARVEME_CARVE found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_DOALL found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_REQUESTDB found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_FIND found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_FINDTRANSPORT found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_DRAFT found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_MEDIUM found in conf/modules.config and Nextflow scripts.
modules_config - GAPSEQ_FILL found in conf/modules.config and Nextflow scripts.
modules_config - MEMOTE_RUN found in conf/modules.config and Nextflow scripts.
modules_config - MEMOTE_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - BACMODEL_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_GAPSEQ_XML 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.

Run details

nf-core/tools version 4.0.2
Run at 2026-07-31 08:44:37

brovolia added 4 commits July 29, 2026 13:22

Addressing comments: use already downloaded db, changes in documentat…

6699f81

…ion, logo

fixing linter error, turn back template for changelog

775a99e

Merge branch 'addressing-comments' into dev

211c87b

# Conflicts: # .nf-core.yml

Trigger CI

3010441

brovolia merged commit e87942f into nf-core:dev Jul 31, 2026
4 checks passed

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Extending db options - #22

Extending db options#22
brovolia merged 5 commits into
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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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