Add BiG-SLiCE to BGC workflow (fresh branch)

[jfy133]

Re-do of #519 but on a fresh branch due a faulty Git merge, but with a fixed module structure for bigslice

All this work was originally done by @SkyLexS

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3fa1dc7

+| ✅ 407 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  13 tests had warnings |!

Details

❗ Test warnings:

• local_component_structure - interproscan_download.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - amp_database_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 - 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 - protein_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - bgc.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 - amp.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
• local_component_structure - cazyme.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

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ 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_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/CONTRIBUTING.md
• 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: 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 ends in dev: 3.1.0dev
• 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.bgc_gecco_convertmode= clusters
• nextflow_config - Config default value correct: params.bgc_gecco_convertformat= gff
• nextflow_config - Config default value correct: params.bgc_bigslice_threshold= 0.4
• nextflow_config - Config default value correct: params.bgc_bigslice_thresholdpct= -1.0
• nextflow_config - Config default value correct: params.bgc_bigslice_nranks= 1
• 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/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_preannotated_cazyme.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_preannotated_cazyme.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_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_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/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_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_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_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_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_prokka.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_prokka.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/test_cazyme_pyrodigal.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_cazyme_pyrodigal.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/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/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 - 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: 25.10.4, Config: 25.10.4
• 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: clean-up.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: labeler.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.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: fix_linting.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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 - GECCO_CONVERT found in conf/modules.config and Nextflow scripts.
• modules_config - BIGSLICE_BIGSLICE found in conf/modules.config and Nextflow scripts.
• modules_config - BIGSLICE_DOWNLOADDB 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.
• modules_config - RUNDBCAN_DATABASE found in conf/modules.config and Nextflow scripts.
• modules_config - RUNDBCAN_CAZYMEANNOTATION found in conf/modules.config and Nextflow scripts.
• modules_config - RUNDBCAN_EASYCGC found in conf/modules.config and Nextflow scripts.
• modules_config - RUNDBCAN_EASYSUBSTRATE 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.
• container_configs - conf/containers_conda_lock_files_amd64.config is up to date
• container_configs - conf/containers_conda_lock_files_arm64.config is up to date
• container_configs - conf/containers_docker_amd64.config is up to date
• container_configs - conf/containers_docker_arm64.config is up to date
• container_configs - conf/containers_singularity_https_amd64.config is up to date
• container_configs - conf/containers_singularity_https_arm64.config is up to date
• container_configs - conf/containers_singularity_oras_amd64.config is up to date
• container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

• nf-core/tools version 4.0.2
• Run at 2026-05-27 11:04:28

[jfy133]

Things missing for you to address @SkyLexS, a couple of minor things but otherwise:

Note I simplified the modules.conf to rely on defaults on .nextflow.conf rather than trying to check within the configuration file manually.

Otherwise only one major thing that is missing:

• Adding BiG-SLiCE to the relevant test configs under conf/ and then in the .nf.test files under `

And then done!