Release: version patch 2.6.1 by Daniel-VM · Pull Request #306 · nf-core/bacass

Daniel-VM · 2026-05-11T15:13:05Z

PR checklist

PR description:

This PR syncs the latest patch changes from dev into master for release 2.6.1.

Main changes:

Restore sample string protection.
Fix KmerFinder taxonomy file selection by using an explicit priority order instead of alphabetical ordering.
Bump pipeline version to 2.6.1.

…betical order

kmerfinder taxonomy file search & Bump version 2.6.1

nf-core-bot · 2026-05-11T15:13:50Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
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 · 2026-05-11T15:16:09Z

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

Posted for pipeline commit 1009e60

+| ✅ 283 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config
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 nextflow.config: Specify any additional parameters here
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/bacass/bacass/subworkflows/local/bakta_dbdownload_run/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ path(versions.yml) ]
_

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config default ignored: params.dfast_config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ 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-bacass_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-bacass_logo_light.png
files_exist - File found: docs/images/nf-core-bacass_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-bacass_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/WorkflowBacass.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 does not contain dev for release: 2.6.1
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.discard_trimmed_pass= false
nextflow_config - Config default value correct: params.long_reads_filtering= porechop
nextflow_config - Config default value correct: params.filtlong_minlen= 10
nextflow_config - Config default value correct: params.rasusa= false
nextflow_config - Config default value correct: params.rasusa_coverage= 100
nextflow_config - Config default value correct: params.assembler= autocycler,canu,dragonflye,flye,megahit,miniasm,unicycler,raven
nextflow_config - Config default value correct: params.autocycler_assemblers= canu,flye,miniasm,raven
nextflow_config - Config default value correct: params.autocycler_subsample_count= 4
nextflow_config - Config default value correct: params.autocycler_subsample_mindepth= 25
nextflow_config - Config default value correct: params.flye_mode= --nano-raw
nextflow_config - Config default value correct: params.busco_lineage= bacteria_odb10
nextflow_config - Config default value correct: params.busco_mode= genome
nextflow_config - Config default value correct: params.busco_clean_intermediates= false
nextflow_config - Config default value correct: params.polish_method= medaka
nextflow_config - Config default value correct: params.annotation_tool= prokka
nextflow_config - Config default value correct: params.baktadb_download_args= --type light
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/
nf_test_content - 'tests/long_rasusa.nf.test' contains outdir parameter
nf_test_content - 'tests/long_rasusa.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_rasusa.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/short_megahit.nf.test' contains outdir parameter
nf_test_content - 'tests/short_megahit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/short_megahit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/dfast.nf.test' contains outdir parameter
nf_test_content - 'tests/dfast.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/dfast.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long.nf.test' contains outdir parameter
nf_test_content - 'tests/long.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_liftoff.nf.test' contains outdir parameter
nf_test_content - 'tests/long_liftoff.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_liftoff.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_autocycler.nf.test' contains outdir parameter
nf_test_content - 'tests/long_autocycler.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_autocycler.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_multiassembler.nf.test' contains outdir parameter
nf_test_content - 'tests/long_multiassembler.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_multiassembler.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_dragonflye.nf.test' contains outdir parameter
nf_test_content - 'tests/long_dragonflye.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_dragonflye.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_type_assembler_compat.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_type_assembler_compat.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_type_assembler_compat.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_type_assembler_compat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hybrid_dragonflye.nf.test' contains outdir parameter
nf_test_content - 'tests/hybrid_dragonflye.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hybrid_dragonflye.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/hybrid.nf.test' contains outdir parameter
nf_test_content - 'tests/hybrid.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hybrid.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_miniasm_prokka.nf.test' contains outdir parameter
nf_test_content - 'tests/long_miniasm_prokka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_miniasm_prokka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_miniasm.nf.test' contains outdir parameter
nf_test_content - 'tests/long_miniasm.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/long_miniasm.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 - assets/nf-core-bacass_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bacass_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bacass_logo_dark.png 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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.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: download_pipeline.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: 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 - NANOPLOT found in conf/modules.config and Nextflow scripts.
modules_config - TOULLIGQC found in conf/modules.config and Nextflow scripts.
modules_config - PYCOQC found in conf/modules.config and Nextflow scripts.
modules_config - PORECHOP_PORECHOP found in conf/modules.config and Nextflow scripts.
modules_config - FILTLONG found in conf/modules.config and Nextflow scripts.
modules_config - AUTOCYCLER_SUBSAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - RASUSA found in conf/modules.config and Nextflow scripts.
modules_config - UNICYCLER found in conf/modules.config and Nextflow scripts.
modules_config - CANU found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_CONSENSUS found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_POLISH found in conf/modules.config and Nextflow scripts.
modules_config - MINIASM found in conf/modules.config and Nextflow scripts.
modules_config - RACON found in conf/modules.config and Nextflow scripts.
modules_config - DRAGONFLYE found in conf/modules.config and Nextflow scripts.
modules_config - MEGAHIT found in conf/modules.config and Nextflow scripts.
modules_config - RAVEN found in conf/modules.config and Nextflow scripts.
modules_config - FLYE found in conf/modules.config and Nextflow scripts.
modules_config - AUTOCYCLER_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - AUTOCYCLER_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - AUTOCYCLER_RESOLVE found in conf/modules.config and Nextflow scripts.
modules_config - AUTOCYCLER_COMBINE found in conf/modules.config and Nextflow scripts.
modules_config - MEDAKA found in conf/modules.config and Nextflow scripts.
modules_config - NANOPOLISH found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_LONG found in conf/modules.config and Nextflow scripts.
modules_config - QUAST found in conf/modules.config and Nextflow scripts.
modules_config - BUSCO_BUSCO found in conf/modules.config and Nextflow scripts.
modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - DFAST found in conf/modules.config and Nextflow scripts.
modules_config - LIFTOFF found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_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.
version_consistency - Version tags are consistent: manifest.version = 2.6.1
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.5.2
Run at 2026-06-04 13:20:55

Sync dev with master

Daniel-VM and others added 8 commits May 11, 2026 09:16

allow sample name to be a sequence of integers

b0cc6b8

update changelog in #305

569ec50

bump version 2.6.1

7d86ea3

fix(kmerfinder): use explicit taxonomy file priority instead of alpha…

2b787f2

…betical order

update changelog in #305

21cb7d8

recover sample string protection

ea80e61

fix changelog in #305

1e1822f

Merge pull request #305 from Daniel-VM/dev

92d5f6d

kmerfinder taxonomy file search & Bump version 2.6.1

Merge master into dev

b6564fd

Daniel-VM mentioned this pull request Jun 4, 2026

Sync dev with master #307

Merged

11 tasks

Merge pull request #307 from Daniel-VM/sync-dev-with-master

1009e60

Sync dev with master

Daniel-VM marked this pull request as ready for review June 4, 2026 13:23

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Release: version patch 2.6.1#306

Release: version patch 2.6.1#306
Daniel-VM wants to merge 10 commits into
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Daniel-VM commented May 11, 2026 •

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❗ Test warnings:

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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Daniel-VM commented May 11, 2026 •

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