Release PR for 3.0.0 #497

jasmezz · 2025-09-18T12:35:25Z

v3.0.0 - French Chocolatine

`Added`

#477, #480, #484 Updated to nf-core template 3.2.1., 3.3.1, 3.3.2 (by @jasmezz, @jfy133)
#482 Added vertical workflow diagram. (by @jasmezz)

`Fixed`

#469 Updated descriptions from 'nextflow_schema.json' and 'schema_input.json'. (by @andreirie)
#471 Fixed fARGene config parameter ext.args. (by @jasmezz)
#479 Fixed ABRicate report file not using correct pipeline sample ID as ID. (fix by @jasmezz, @jfy133)
#486 Updated argNorm citation. (by @Vedanth-Ramji, @jasmezz)

`Dependencies`

Tool	Previous Version	New Version
antiSMASH	7.1.0	8.0.1
RGI	6.0.3	6.0.5

`Deprecated`

#478 Removed --bgc_antismash_installdir as new antiSMASH module container no longer requires mounting of this directory for execution. (by @mberacochea and @jfy133)

PR checklist

Post release version bump

…on'.

Switch-to-self-hosted-runners

Json schema improvements

…rgene

Fix fARGene config param

Add CODEOWNERs file for active maintainers

Important! Template update for nf-core/tools v3.2.1

…eter

Bump version 3.0.0

github-actions · 2025-09-18T12:38:06Z

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

Posted for pipeline commit 1b1a8fc

+| ✅ 390 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

local_component_structure - amp_database_download.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - merge_taxonomy_ampcombi.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - merge_taxonomy_hamronization.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - interproscan_download.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - combgc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - merge_taxonomy_combgc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - bgc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - protein_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - arg.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - amp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - taxa_class.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.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: 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-funcscan_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-funcscan_logo_light.png
files_exist - File found: docs/images/nf-core-funcscan_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-funcscan_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/WorkflowFuncscan.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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 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: 3.0.0
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.taxa_classification_tool= mmseqs2
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_db_id= Kalamari
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_searchtype= 2
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcaranks= kingdom,phylum,class,order,family,genus,species
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_taxlineage= 1
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_sensitivity= 5.0
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_orffilters= 2.0
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcamode= 3
nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_votemode= 1
nextflow_config - Config default value correct: params.annotation_tool= pyrodigal
nextflow_config - Config default value correct: params.annotation_bakta_db_downloadtype= full
nextflow_config - Config default value correct: params.annotation_bakta_mincontiglen= 1
nextflow_config - Config default value correct: params.annotation_bakta_translationtable= 11
nextflow_config - Config default value correct: params.annotation_bakta_gram= ?
nextflow_config - Config default value correct: params.annotation_prokka_kingdom= Bacteria
nextflow_config - Config default value correct: params.annotation_prokka_gcode= 11
nextflow_config - Config default value correct: params.annotation_prokka_mincontiglen= 1
nextflow_config - Config default value correct: params.annotation_prokka_evalue= 1e-06
nextflow_config - Config default value correct: params.annotation_prokka_coverage= 80
nextflow_config - Config default value correct: params.annotation_prokka_compliant= true
nextflow_config - Config default value correct: params.annotation_prodigal_transtable= 11
nextflow_config - Config default value correct: params.annotation_pyrodigal_transtable= 11
nextflow_config - Config default value correct: params.protein_annotation_tool= InterProScan
nextflow_config - Config default value correct: params.protein_annotation_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.protein_annotation_interproscan_applications= PANTHER,ProSiteProfiles,ProSitePatterns,Pfam
nextflow_config - Config default value correct: params.amp_ampir_model= precursor
nextflow_config - Config default value correct: params.amp_ampir_minlength= 10
nextflow_config - Config default value correct: params.amp_ampcombi_db_id= DRAMP
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_cutoff= 0.6
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_aalength= 120
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_dbevalue= 5.0
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_hmmevalue= 0.06
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_windowstopcodon= 60
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_windowtransport= 11
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_ampir= .ampir.tsv
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_amplify= .amplify.tsv
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_macrel= .macrel.prediction
nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_hmmsearch= .hmmer_hmmsearch.txt
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_covmode= 0.0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_sensitivity= 4.0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_minmembers= 0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_mode= 1.0
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_coverage= 0.8
nextflow_config - Config default value correct: params.amp_ampcombi_cluster_seqid= 0.4
nextflow_config - Config default value correct: params.arg_amrfinderplus_identmin= -1.0
nextflow_config - Config default value correct: params.arg_amrfinderplus_coveragemin= 0.5
nextflow_config - Config default value correct: params.arg_amrfinderplus_translationtable= 11
nextflow_config - Config default value correct: params.arg_deeparg_db_version= 2
nextflow_config - Config default value correct: params.arg_deeparg_model= LS
nextflow_config - Config default value correct: params.arg_deeparg_minprob= 0.8
nextflow_config - Config default value correct: params.arg_deeparg_alignmentevalue= 1e-10
nextflow_config - Config default value correct: params.arg_deeparg_alignmentidentity= 50
nextflow_config - Config default value correct: params.arg_deeparg_alignmentoverlap= 0.8
nextflow_config - Config default value correct: params.arg_deeparg_numalignmentsperentry= 1000
nextflow_config - Config default value correct: params.arg_fargene_hmmmodel= class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme
nextflow_config - Config default value correct: params.arg_fargene_minorflength= 90
nextflow_config - Config default value correct: params.arg_fargene_translationformat= pearson
nextflow_config - Config default value correct: params.arg_rgi_alignmenttool= BLAST
nextflow_config - Config default value correct: params.arg_rgi_data= NA
nextflow_config - Config default value correct: params.arg_rgi_split_prodigal_jobs= true
nextflow_config - Config default value correct: params.arg_abricate_db_id= ncbi
nextflow_config - Config default value correct: params.arg_abricate_minid= 80
nextflow_config - Config default value correct: params.arg_abricate_mincov= 80
nextflow_config - Config default value correct: params.arg_hamronization_summarizeformat= tsv
nextflow_config - Config default value correct: params.bgc_mincontiglength= 3000
nextflow_config - Config default value correct: params.bgc_antismash_contigminlength= 3000
nextflow_config - Config default value correct: params.bgc_antismash_hmmdetectionstrictness= relaxed
nextflow_config - Config default value correct: params.bgc_antismash_taxon= bacteria
nextflow_config - Config default value correct: params.bgc_deepbgc_score= 0.5
nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxproteingap= 0
nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxnuclgap= 0
nextflow_config - Config default value correct: params.bgc_deepbgc_minnucl= 1
nextflow_config - Config default value correct: params.bgc_deepbgc_minproteins= 1
nextflow_config - Config default value correct: params.bgc_deepbgc_mindomains= 1
nextflow_config - Config default value correct: params.bgc_deepbgc_minbiodomains= 0
nextflow_config - Config default value correct: params.bgc_deepbgc_classifierscore= 0.5
nextflow_config - Config default value correct: params.bgc_gecco_cds= 3
nextflow_config - Config default value correct: params.bgc_gecco_pfilter= 1e-09
nextflow_config - Config default value correct: params.bgc_gecco_threshold= 0.8
nextflow_config - Config default value correct: params.bgc_gecco_edgedistance= 0
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/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/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_preannotated_bgc.nf.test' contains outdir parameter
nf_test_content - 'tests/test_preannotated_bgc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_bgc_prokka.nf.test' contains outdir parameter
nf_test_content - 'tests/test_bgc_prokka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_minimal.nf.test' contains outdir parameter
nf_test_content - 'tests/test_minimal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_prokka.nf.test' contains outdir parameter
nf_test_content - 'tests/test_prokka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_bgc_bakta.nf.test' contains outdir parameter
nf_test_content - 'tests/test_bgc_bakta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_bgc_pyrodigal.nf.test' contains outdir parameter
nf_test_content - 'tests/test_bgc_pyrodigal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_preannotated.nf.test' contains outdir parameter
nf_test_content - 'tests/test_preannotated.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_bakta.nf.test' contains outdir parameter
nf_test_content - 'tests/test_bakta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_taxonomy_pyrodigal.nf.test' contains outdir parameter
nf_test_content - 'tests/test_taxonomy_pyrodigal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_taxonomy_bakta.nf.test' contains outdir parameter
nf_test_content - 'tests/test_taxonomy_bakta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_taxonomy_prokka.nf.test' contains outdir parameter
nf_test_content - 'tests/test_taxonomy_prokka.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/PULL_REQUEST_TEMPLATE.md 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-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_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: 24.10.5, Config: 24.10.5
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: 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'
base_config - conf/base.config found and not ignored.
base_config - GUNZIP found in conf/base.config and Nextflow scripts.
base_config - UNTAR found in conf/base.config and Nextflow scripts.
base_config - PROKKA found in conf/base.config and Nextflow scripts.
base_config - PRODIGAL_GBK found in conf/base.config and Nextflow scripts.
base_config - BAKTA_BAKTA found in conf/base.config and Nextflow scripts.
base_config - ABRICATE_RUN found in conf/base.config and Nextflow scripts.
base_config - AMRFINDERPLUS_RUN found in conf/base.config and Nextflow scripts.
base_config - DEEPARG_DOWNLOADDATA found in conf/base.config and Nextflow scripts.
base_config - DEEPARG_PREDICT found in conf/base.config and Nextflow scripts.
base_config - FARGENE found in conf/base.config and Nextflow scripts.
base_config - RGI_MAIN found in conf/base.config and Nextflow scripts.
base_config - AMPIR found in conf/base.config and Nextflow scripts.
base_config - AMPLIFY_PREDICT found in conf/base.config and Nextflow scripts.
base_config - AMP_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
base_config - MACREL_CONTIGS found in conf/base.config and Nextflow scripts.
base_config - BGC_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
base_config - ANTISMASH_ANTISMASH found in conf/base.config and Nextflow scripts.
base_config - ANTISMASH_ANTISMASHDOWNLOADDATABASES found in conf/base.config and Nextflow scripts.
base_config - DEEPBGC_DOWNLOAD found in conf/base.config and Nextflow scripts.
base_config - DEEPBGC_PIPELINE found in conf/base.config and Nextflow scripts.
base_config - GECCO_RUN found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_ABRICATE found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_DEEPARG found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_RGI found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_FARGENE found in conf/base.config and Nextflow scripts.
base_config - HAMRONIZATION_SUMMARIZE found in conf/base.config and Nextflow scripts.
base_config - ARGNORM_DEEPARG found in conf/base.config and Nextflow scripts.
base_config - ARGNORM_ABRICATE found in conf/base.config and Nextflow scripts.
base_config - ARGNORM_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
base_config - AMPCOMBI2_PARSETABLES found in conf/base.config and Nextflow scripts.
base_config - AMPCOMBI2_CLUSTER found in conf/base.config and Nextflow scripts.
base_config - INTERPROSCAN_DATABASE found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_DATABASES found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_CREATEDB found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_TAXONOMY found in conf/modules.config and Nextflow scripts.
modules_config - MMSEQS_CREATETSV found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SEQ_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SEQ_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - INTERPROSCAN_DATABASE found in conf/modules.config and Nextflow scripts.
modules_config - INTERPROSCAN found in conf/modules.config and Nextflow scripts.
modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTADBDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
modules_config - PRODIGAL found in conf/modules.config and Nextflow scripts.
modules_config - PYRODIGAL found in conf/modules.config and Nextflow scripts.
modules_config - ABRICATE_RUN found in conf/modules.config and Nextflow scripts.
modules_config - AMRFINDERPLUS_UPDATE found in conf/modules.config and Nextflow scripts.
modules_config - AMRFINDERPLUS_RUN found in conf/modules.config and Nextflow scripts.
modules_config - DEEPARG_DOWNLOADDATA found in conf/modules.config and Nextflow scripts.
modules_config - DEEPARG_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - FARGENE found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_CARD found in conf/modules.config and Nextflow scripts.
modules_config - RGI_CARDANNOTATION found in conf/modules.config and Nextflow scripts.
modules_config - RGI_MAIN found in conf/modules.config and Nextflow scripts.
modules_config - AMPIR found in conf/modules.config and Nextflow scripts.
modules_config - AMPLIFY_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - AMP_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
modules_config - MACREL_CONTIGS found in conf/modules.config and Nextflow scripts.
modules_config - BGC_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
modules_config - ANTISMASH_ANTISMASH found in conf/modules.config and Nextflow scripts.
modules_config - ANTISMASH_ANTISMASHDOWNLOADDATABASES found in conf/modules.config and Nextflow scripts.
modules_config - DEEPBGC_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - DEEPBGC_PIPELINE found in conf/modules.config and Nextflow scripts.
modules_config - GECCO_RUN found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_ABRICATE found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_DEEPARG found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_RGI found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_FARGENE found in conf/modules.config and Nextflow scripts.
modules_config - HAMRONIZATION_SUMMARIZE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_TAXONOMY_HAMRONIZATION found in conf/modules.config and Nextflow scripts.
modules_config - ARG_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - AMPCOMBI2_PARSETABLES found in conf/modules.config and Nextflow scripts.
modules_config - AMPCOMBI2_COMPLETE found in conf/modules.config and Nextflow scripts.
modules_config - AMPCOMBI2_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_TAXONOMY_AMPCOMBI found in conf/modules.config and Nextflow scripts.
modules_config - AMP_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - COMBGC found in conf/modules.config and Nextflow scripts.
modules_config - ARGNORM_ABRICATE found in conf/modules.config and Nextflow scripts.
modules_config - ARGNORM_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
modules_config - ARGNORM_DEEPARG found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_TAXONOMY_COMBGC found in conf/modules.config and Nextflow scripts.
modules_config - BGC_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
modules_config - AMP_DATABASE_DOWNLOAD 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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 3.0.0, nfcore_yml.version = 3.0.0

Run details

nf-core/tools version 3.3.2
Run at 2025-10-04 18:57:52

docs/images/funcscan_metro_workflow_vertical.png

tests/default.nf.test

maxulysse

Looks good to me.
Only minor things that could be improved on the testing side, but I know how long it can take, so no issue from me there

docs/usage.md

tests/default.nf.test

jfy133 · 2025-09-18T13:24:59Z

tests/default.nf.test.snap

+                },
+                "AMRFINDERPLUS_RUN": {
+                    "amrfinderplus": "3.12.8",
+                    "amrfinderplus-database": null


Minor thing for the future,, we should fix that

Fix conda CI errors

jfy133 · 2025-09-20T07:33:11Z

That AI review request was a mistake, please disregard

Copilot

Pull Request Overview

This release PR for v3.0.0 "French Chocolatine" updates the nf-core/funcscan pipeline with significant infrastructure and dependency changes. The PR includes updates to the nf-core template (3.2.1 → 3.3.2), upgrades antiSMASH (7.1.0 → 8.0.1) and RGI (6.0.3 → 6.0.5), and removes the deprecated --bgc_antismash_installdir parameter.

Updated to nf-core template 3.3.2 with modernized CI/CD workflows
Upgraded antiSMASH to v8.0.1 and RGI to v6.0.5 for improved functionality
Fixed ABRicate sample ID handling and fARGene configuration issues

Reviewed Changes

Copilot reviewed 113 out of 120 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/*.nf.test	Updated test files with new profile declarations and fixed log file paths
modules/nf-core/antismash/*	Replaced antismashlite modules with full antismash implementation
modules/nf-core/rgi/*	Updated RGI modules to version 6.0.5
modules/nf-core/abricate/run/*	Fixed sample ID handling in ABRicate output
.github/workflows/*	Modernized CI/CD with nf-test framework replacing older CI approach
conf/*.config	Added antismash database parameters and updated resource limits
nextflow.config	Updated version to 3.0.0 and removed deprecated parameters

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

tests/test_taxonomy_pyrodigal.nf.test

subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf

nextflow_schema.json

Co-authored-by: Copilot <[email protected]>

jfy133 · 2025-09-23T08:02:42Z

The error:

d7/123ea9] process > NFCORE_FUNCSCAN:FUNCSCAN:ARG:HAMRONIZATION_ABRICATE (sample_1)                                          [100%] 2 of 2 ✔
Plus 4 more processes waiting for tasks…
Creating env using conda: /home/james/git/nf-core/funcscan/modules/nf-core/rgi/main/environment.yml [cache /home/james/cache/conda/env-30d4b66be29ab9cc-249b7045e8490b1f08623b5f3fec6d6a]
[12/a9c982] NOTE: Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_1)` terminated with an error exit status (1) -- Execution is retried (1)
[72/ae1ca2] NOTE: Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_2)` terminated with an error exit status (1) -- Execution is retried (1)
[e3/25e0f1] NOTE: Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_1)` terminated with an error exit status (1) -- Execution is retried (2)
[08/78acb1] NOTE: Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_2)` terminated with an error exit status (1) -- Execution is retried (2)
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_1)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (sample_1)` terminated with an error exit status (1)


Command executed:

  ampcombi parse_tables \
      --path_list 'sample_1.amplify.tsv' 'sample_1.ampir.tsv' 'sample_1.macrel.prediction' \
      --faa sample_1_pyrodigal.faa \
      --gbk sample_1_pyrodigal.gbk \
      --sample_list sample_1 \
      --amp_database DRAMP \
      --amp_database_dir amp_DRAMP_database \
       \
      --aminoacid_length 120 --db_evalue 5 --amp_cutoff 0.6 --ampir_file .ampir.tsv --amplify_file .amplify.tsv --macrel_file .macrel.prediction --hmmsearch_file .hmmer_hmmsearch.txt --ampgram_file '.tsv' --amptransformer_file '.txt' --neubi_file '.fasta' --log TRUE --hmm_evalue 0.06 --window_size_stop_codon 60 --window_size_transporter 11 \
      --threads 4
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES":
      ampcombi: $(ampcombi --version | sed 's/ampcombi //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/ampcombi", line 10, in <module>
      sys.exit(main())
               ^^^^^^
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/ampcombi.py", line 492, in main
      args.func(args)  # call the default function
      ^^^^^^^^^^^^^^^
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/ampcombi.py", line 467, in parse_table_log
      log_output('Ampcombi_parse_tables.log', args, parse_tables)
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/ampcombi.py", line 453, in log_output
      func(args)
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/ampcombi.py", line 258, in parse_tables
      process_sample(
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/ampcombi.py", line 318, in process_sample
      mmseqs_df = mmseq_alignment_merge(db, amp_faa_paths, amp_matches, threads, dbevalue, summary_df_filtered, sample)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/james/cache/conda/env-9addea70043a1a7f-a9e8ec1556d51be57f9eecb3ab4462f5/bin/amp_database.py", line 235, in mmseq_alignment_merge
      if (os.stat(mmseqs_search_path).st_size == 0):
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

Work dir:
  /home/james/git/nf-core/funcscan/testing/work/ce/ad5fc103a1c252f73d256ccb9cc57d

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/funcscan] Pipeline completed with errors-

jfy133 · 2025-10-04T11:14:15Z

Finally 🎉 was a space issue!

jfy133 · 2025-10-04T11:14:54Z

I'm just going to update AMRFinderplus & hAMRonization accordingly, and then we are good to go :)

CHANGELOG.md

jasmezz and others added 30 commits March 5, 2025 14:18

Post release version bump + changelog update

94ecd83

Merge pull request #465 from nf-core/post-release-version-bump

1f7c97e

Post release version bump

Merge branch 'nf-core:master' into json-schema-improvements

3d9fffa

Changed descriptions from 'nextflow_schema.json' and 'schema_input.js…

a631806

…on'.

switch to self-hosted-runners

ed75e46

Merge pull request #470 from nf-core/switch-to-self-hosted-runners

3b0faf6

Switch-to-self-hosted-runners

Updated changelog

e96be7b

Updated CHANGELOG.md

bd45649

bump changelog

c83c2fc

Bump changelog

6c9d13f

Fixed changelog

6a2c09b

Fixed changelod

079f217

Merge pull request #469 from andreirie/json-schema-improvements

29c1fad

Json schema improvements

Fix fARGene config, update changelog

65fc49b

[automated] Fix code linting

9c4fbbb

Update notation

9aee323

Update ci.yml

63673c4

Merge branch 'fix-fargene' of github.com:nf-core/funcscan into fix-fa…

40c0ef7

…rgene

Update nf-test files

4442765

Merge pull request #471 from nf-core/fix-fargene

cf3a501

Fix fARGene config param

Add CODEOWNERs file

2b34366

Merge pull request #476 from nf-core/add-codeowners-file

7063ce2

Add CODEOWNERs file for active maintainers

Template update for nf-core/tools version 3.2.1

26ca22f

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

178bf4a

Fix space

810ce2a

Update changelog

c119717

Update nextflow.config

ced7c7d

Merge pull request #477 from nf-core/nf-core-template-merge-3.2.1

0ad0147

Important! Template update for nf-core/tools v3.2.1

Update antiSMASH to v8 and drop now unrequired installation dir param…

29467b2

…eter

Apply suggestions from code review

798f864

jfy133 and others added 5 commits September 17, 2025 11:18

Update workflow PNGs

675b5e5

[automated] Fix code linting

83613c1

Update version in snapshot

3c85fe8

Update CHANGELOG.md [skip ci]

c84c53c

Merge pull request #495 from nf-core/bump-version-3.0.0

02acf4e

Bump version 3.0.0

maxulysse reviewed Sep 18, 2025

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maxulysse reviewed Sep 18, 2025

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maxulysse approved these changes Sep 18, 2025

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jfy133 approved these changes Sep 18, 2025

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jfy133 and others added 4 commits September 19, 2025 09:54

Update docs/usage.md

a4ba298

Fix conda CI errors

c1db8d2

Update CHANGELOG.md

17ab9f0

Merge pull request #498 from nf-core/fix-conda-ci-errors

34c8b3c

Fix conda CI errors

jfy133 requested a review from Copilot September 20, 2025 07:32

Copilot AI reviewed Sep 20, 2025

View reviewed changes

Apply suggestions from code review

c779f8a

Co-authored-by: Copilot <[email protected]>

jfy133 added 4 commits September 23, 2025 10:13

Fix mistake in html

78e557f

Update AMRFINDERPLUS to latest (and thus latest version)

b66d69f

Use larger runner for tests

aae69ac

Use larger runner

c3be6fd

jfy133 added 2 commits October 4, 2025 15:06

Update amrfinderplus and hAMRonization

f082be6

Merge branch 'dev' of github.com:nf-core/funcscan into dev

6ecdffb

jfy133 reviewed Oct 4, 2025

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CHANGELOG.md Show resolved Hide resolved

Apply suggestion from @jfy133

1b1a8fc

jfy133 merged commit fa9db01 into master Oct 4, 2025
74 of 79 checks passed

Release PR for 3.0.0 #497

Release PR for 3.0.0 #497

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jasmezz commented Sep 18, 2025

v3.0.0 - French Chocolatine

Added

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Dependencies

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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Pull Request Overview

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jfy133 commented Sep 23, 2025

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github-actions bot commented Sep 18, 2025 •

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