Update mtromap by jfy133 · Pull Request #522 · nf-core/funcscan

jfy133 · 2026-03-24T04:20:39Z

Updates standard horizontal metro-map to include CAZyme analysis

I didn't do the vertical one to (just renamed it to mention which version it represented), because it takes too much time to update these😅. Side note though, if we want to make having the two easier, nf-metro should be investigated.

PR checklist

github-actions · 2026-03-24T04:23:40Z

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

Posted for pipeline commit 9239f9a

+| ✅ 395 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  13 tests had warnings |!

Details

❗ Test warnings:

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_combgc.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_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 - 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 - cazyme.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 - annotation.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 fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.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-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: 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.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_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_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_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_preannotated.nf.test' contains outdir parameter
nf_test_content - 'tests/test_preannotated.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/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_minimal.nf.test' contains outdir parameter
nf_test_content - 'tests/test_minimal.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_bakta.nf.test' contains outdir parameter
nf_test_content - 'tests/test_bakta.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_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_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_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/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 - 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: 25.04.0, Config: 25.04.0
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: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: labeler.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 - 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: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-24 04:23:25

jfy133 added 2 commits March 24, 2026 05:16

Update mtromap

8112e99

Minor fixes

9239f9a

jfy133 requested review from Darcy220606 and jasmezz as code owners March 24, 2026 04:20

github-actions bot added the size/xl label Mar 24, 2026

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Update mtromap#522

Update mtromap#522
jfy133 wants to merge 2 commits intodevfrom
3.1-metromap

jfy133 commented Mar 24, 2026

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github-actions bot commented Mar 24, 2026

❗ Test warnings:

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jfy133 commented Mar 24, 2026

PR checklist

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github-actions bot commented Mar 24, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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