funcscan Fix staging of custom HMMs for Bakta

Fix staging of custom HMMs for Bakta

Open jfy133 opened this issue 1 month ago • 3 comments

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).

Oct 23 '25 13:10 jfy133

This PR is against the `master` branch :x:

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/funcscan master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the nf-core/funcscan dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

Oct 23 '25 13:10 github-actions[bot]

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 34c962c

+| ✅ 385 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  12 tests had warnings |!

:heavy_exclamation_mark: 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

:grey_question: Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config

:white_check_mark: 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.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: 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: 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: 3.4.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.4.1
Run at 2025-10-23 13:37:09

Oct 23 '25 13:10 github-actions[bot]

@nf-core-bot fix linting

Oct 23 '25 13:10 jfy133

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Fix staging of custom HMMs for Bakta

PR checklist

This PR is against the master branch :x:

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

:heavy_exclamation_mark: Test warnings:

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

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This PR is against the `master` branch :x:

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning: