Important! Template update for nf-core/tools v2.14.1

[nf-core-bot]

Version 2.14.1 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-2.14.1 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 v2.14.1 release page.

[github-actions]

nf-core lint overall result: Passed ✅

Posted for pipeline commit 5ad3cde

+| ✅ 317 tests passed       |+

✅ 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: conf/igenomes.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 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 - 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: params.validationShowHiddenParams
• nextflow_config - Config variable found: params.validationSchemaIgnoreParams
• 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 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: 1.2.0dev
• 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.contig_qc_lengththreshold= 3000.0
• nextflow_config - Config default value correct: params.taxa_classification_tool= mmseqs2
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_databases_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.amp_ampir_model= precursor
• nextflow_config - Config default value correct: params.amp_ampir_minlength= 10
• nextflow_config - Config default value correct: params.amp_ampcombi_cutoff= 0.0
• 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_data_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_savejson= false
• nextflow_config - Config default value correct: params.arg_rgi_savetmpfiles= false
• nextflow_config - Config default value correct: params.arg_rgi_alignmenttool= BLAST
• nextflow_config - Config default value correct: params.arg_rgi_includeloose= false
• nextflow_config - Config default value correct: params.arg_rgi_includenudge= false
• nextflow_config - Config default value correct: params.arg_rgi_lowquality= false
• 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= 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.bgc_antismash_contigminlength= 1000
• 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.arg_hamronization_summarizeformat= tsv
• 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.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• 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_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.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: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (310 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: awstest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.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_GFF 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 - AMPCOMBI 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 - SEQKIT_SEQ_LONG found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SEQ_SHORT 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 - 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_GFF found in conf/modules.config and Nextflow scripts.
• modules_config - PRODIGAL_GBK 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 - AMPCOMBI 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 - 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 - DRAMP_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: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-05-15 10:27:07

[jfy133]

LGTM, would be nice to have second pair of eyes

[JoseEspinosa]

LGTM! 🚀

[JoseEspinosa]

LGTM! 🚀

Ups... but not to CI

[jfy133]

LGTM! 🚀

Ups... but not to CI

Download failure, will restart in a bit (previous run passed as you can see above)