Important! Template update for nf-core/tools v3.2.1 #477

nf-core-bot · 2025-04-30T12:26:01Z

Version 3.2.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.2.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.2.1 release page.

github-actions · 2025-04-30T13:01:00Z

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

Posted for pipeline commit ced7c7d

+| ✅ 351 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  12 tests had warnings |!

❗ Test warnings:

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 - 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 - arg.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 - annotation.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 - protein_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
actions_ci - actions_ci

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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/ci.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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-funcscan_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowFuncscan.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 2.2.0dev
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_compressed= 0
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/
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_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO 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: 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: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
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_ANTISMASHLITE found in conf/base.config and Nextflow scripts.
base_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES 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_ANTISMASHLITE found in conf/modules.config and Nextflow scripts.
modules_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES 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: 3.2.1

Run details

nf-core/tools version 3.2.1
Run at 2025-05-07 08:53:32

ro-crate-metadata.json

jonasscheid · 2025-05-02T06:34:30Z

Do the failed tests run through locally? I would say its fine to merge if yes. For the future: Is be possible to reduce the number of pulled containers?

nextflow.config

jfy133 · 2025-05-07T08:53:25Z

Do the failed tests run through locally? I would say its fine to merge if yes. For the future: Is be possible to reduce the number of pulled containers?

I'm investigating this now.

nf-test test --tag test_taxonomy_bakta --profile test_taxonomy_bakta,docker

Doesn't run on gitpod as that is producing >30GB in the .nf-test/test/ folder. I'm investigating wher eit is coming from

jfy133 · 2025-05-07T09:25:24Z

By far the largest files are:

3.7G    ./3b
3.7G    ./3b/64fdfd010293a14d3c12ebfe0259b7
3.7G    ./3b/64fdfd010293a14d3c12ebfe0259b7/db-light
9.4G    ./2f/a84322d08d913d4cb998428d2631f7/antismash_db
9.7G    ./2f
9.7G    ./2f/a84322d08d913d4cb998428d2631f7
18G     .

Which are bakta (4gb) and antismash (10GB).

jfy133 · 2025-05-07T11:00:57Z

@mberacochea has pointed me towards a 'small' version of the antismash database we can potentially use! I will try that

jfy133 · 2025-05-07T12:43:15Z

I'm going to merge this now and investigate the size thing separately, as we have #475 - maybe can do a big overhaul

Template update for nf-core/tools version 3.2.1

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nf-core-bot requested review from Darcy220606, jasmezz and jfy133 as code owners April 30, 2025 12:26

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

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jasmezz reviewed Apr 30, 2025

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jasmezz and others added 2 commits April 30, 2025 13:06

Fix space

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Update changelog

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jfy133 reviewed May 7, 2025

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Update nextflow.config

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jfy133 self-requested a review May 7, 2025 12:42

jfy133 approved these changes May 7, 2025

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jfy133 merged commit 0ad0147 into dev May 22, 2025
26 of 30 checks passed

jfy133 deleted the nf-core-template-merge-3.2.1 branch May 22, 2025 14:14

jasmezz mentioned this pull request Sep 18, 2025

Release PR for 3.0.0 #497

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Important! Template update for nf-core/tools v3.2.1 #477

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