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Activate CAZyme analysis in full test#523

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jfy133 wants to merge 1 commit intodevfrom
cazyme-in-fulltest
Draft

Activate CAZyme analysis in full test#523
jfy133 wants to merge 1 commit intodevfrom
cazyme-in-fulltest

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@jfy133 jfy133 commented Mar 30, 2026

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).

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 913a7b9

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

❗ Test warnings:

❔ 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:

✅ 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_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_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_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_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_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_bakta.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_bakta.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_bgc_prokka.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_bgc_prokka.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_bgc_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.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_preannotated.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_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_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/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/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: download_pipeline.yml
  • actions_schema_validation - Workflow validation passed: labeler.yml
  • actions_schema_validation - Workflow validation passed: nf-test.yml
  • actions_schema_validation - Workflow validation passed: linting.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: branch.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: release-announcements.yml
  • actions_schema_validation - Workflow validation passed: fix_linting.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 - 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 2026-03-30 06:48:18

Comment on lines +30 to +31
amp_skip_amplify = true
// takes too long
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Suggested change
amp_skip_amplify = true
// takes too long
amp_skip_amplify = true // takes too long

Unless there is a recommendation to have comment in separate line?

Comment on lines +44 to +45
bgc_skip_deepbgc = true
// takes too long
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Suggested change
bgc_skip_deepbgc = true
// takes too long
bgc_skip_deepbgc = true // takes too long

@jfy133 jfy133 marked this pull request as draft March 30, 2026 07:16
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jfy133 commented Mar 30, 2026

Failed first attempt on default, trying increased memory

@jfy133
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jfy133 commented Mar 30, 2026

@HaidYi @Xinpeng021001 when running our full test on our wastewater test data (which might not be super optimal), I got the following error:

Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:CAZYME:RUNDBCAN_EASYSUBSTRATE (ERZ1664507)'

Caused by:
  Missing output file(s) `ERZ1664507_synteny_pdf/` expected by process `NFCORE_FUNCSCAN:FUNCSCAN:CAZYME:RUNDBCAN_EASYSUBSTRATE (ERZ1664507)`


Command executed:

  run_dbcan easy_substrate \
      --mode protein \
      --db_dir dbcan_db \
      --input_raw_data ERZ1664507_pyrodigal.faa \
      --output_dir . \
      --input_gff ERZ1664507_pyrodigal.gff \
      --gff_type prodigal \
  
  
  mv overview.tsv             ERZ1664507_overview.tsv
  mv dbCAN_hmm_results.tsv    ERZ1664507_dbCAN_hmm_results.tsv
  mv dbCANsub_hmm_results.tsv ERZ1664507_dbCANsub_hmm_results.tsv
  mv diamond.out              ERZ1664507_diamond.out
  mv cgc.gff                  ERZ1664507_cgc.gff
  mv cgc_standard_out.tsv     ERZ1664507_cgc_standard_out.tsv
  mv diamond.out.tc           ERZ1664507_diamond.out.tc
  mv STP_hmm_results.tsv      ERZ1664507_STP_hmm_results.tsv
  mv total_cgc_info.tsv       ERZ1664507_total_cgc_info.tsv
  mv CGC.faa                  ERZ1664507_CGC.faa
  mv PUL_blast.out            ERZ1664507_PUL_blast.out
  mv substrate_prediction.tsv ERZ1664507_substrate_prediction.tsv
  mv synteny_pdf/             ERZ1664507_synteny_pdf/
  if [ -f TF_hmm_results.tsv ]; then
      mv TF_hmm_results.tsv   ERZ1664507_TF_hmm_results.tsv
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:CAZYME:RUNDBCAN_EASYSUBSTRATE":
      dbcan: $(echo $(run_dbcan version) | cut -f2 -d':' | cut -f2 -d' ')
  END_VERSIONS

Command exit status:
  0

Command output:
  step 1/4  CAZyme annotation...
  step 2/4  GFF processing...
  step 3/4  CGC identification...
  step 4/4  Substrate prediction...
  CGC substrate analysis completed.

Command error:
  
  Generating Prodigal GFF: 0it [00:00, ?it/s]
  Generating Prodigal GFF: 1it [00:07,  7.79s/it]
  Generating Prodigal GFF: 18818it [00:07, 2379.85it/s]
  2026-03-30 07:39:34,101 - dbcan.plot.syntenic_plot - WARNING - [diagnostic]error candidate=0, blast_groups=21, CGC=9, PUL=633. missing_cgc=0, missing_pul=0, no_blast=0

Work dir:
  s3://nf-core-awsmegatests/work/funcscan/work-913a7b90c96d187040fb0cbb59621afb04b6beff/cf/407aa76cfc8f8adc29c0cfe64f8175

Container:
  wave.seqera.io/wt/78326257ad28/biocontainers/dbcan:5.2.6--pyhdfd78af_0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Is this a valid output or does it suggest something went wrong? Should we make the PDf outputs optional in the module?

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