Report BUSCO errors

[muffato]

Closes #178

My solution is simply to return a non-zero code if there is "Run failed; check logs" in the output file.

Note that this leaves Prodigal errors off the hook, as these are reported as "No genes found" (cf #147 (comment))

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
• 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).

[sanger-tolsoft]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1bba35c

+| ✅ 187 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗  19 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 0.8.1
• local_component_structure - windowstats_input.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - restructurebuscodir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - generate_config.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - create_bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - compressblobdir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - jsonify_taxdump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - nohit_list.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - view.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - run_blastx.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - blobtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - collate_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - run_blastn.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - busco_diamond_blastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - finalise_blobdir.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - coverage_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - minimap_alignment.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: conf/igenomes.config
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
• template_strings - template_strings
• merge_markers - merge_markers

✅ 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: 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/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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• 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_ignored.config
• 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-blobtoolkit_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/WorkflowBlobtoolkit.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.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• 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.image_format= png
• nextflow_config - Config default value correct: params.outdir= results
• 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
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml 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
• 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
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: sanger_test.yml
• actions_schema_validation - Workflow validation passed: sanger_test_full.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• 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 '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 - WINDOWSTATS_INPUT found in conf/base.config and Nextflow scripts.
• base_config - BLOBTOOLKIT_WINDOWSTATS found in conf/base.config and Nextflow scripts.
• base_config - FASTAWINDOWS found in conf/base.config and Nextflow scripts.
• base_config - BUSCO_BUSCO found in conf/base.config and Nextflow scripts.
• base_config - BLAST_BLASTN found in conf/base.config and Nextflow scripts.
• base_config - NOHIT_LIST found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - WINDOWMASKER_MKCOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - WINDOWMASKER_USTAT found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_HIC found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ILMN found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_CCS found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_CLR found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ONT found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - PIGZ_COMPRESS found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTK_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - BUSCO_BUSCO found in conf/modules.config and Nextflow scripts.
• modules_config - RESTRUCTUREBUSCODIR found in conf/modules.config and Nextflow scripts.
• modules_config - DIAMOND_BLASTP found in conf/modules.config and Nextflow scripts.
• modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTK_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTOOLKIT_WINDOWSTATS found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTOOLKIT_CREATEBLOBDIR found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTOOLKIT_UPDATEBLOBDIR found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTOOLKIT_CHUNK found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTOOLKIT_UNCHUNK found in conf/modules.config and Nextflow scripts.
• modules_config - NOHIT_LIST found in conf/modules.config and Nextflow scripts.
• modules_config - BLAST_BLASTN found in conf/modules.config and Nextflow scripts.
• modules_config - COMPRESSBLOBDIR found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTK_IMAGES found in conf/modules.config and Nextflow scripts.
• modules_config - JSONIFY_TAXDUMP found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC 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 2025-08-22 14:01:10

[DLBPointon]

LGTM

If this is as wide spread an issue as the attached issue implies, then would it make sense to push up to nf-core too? Surely there will be people in the same boat?

[muffato]

If this is as wide spread an issue as the attached issue implies, then would it make sense to push up to nf-core too? Surely there will be people in the same boat?

Good call. Mahesh was happy to approve the request :)

I've force-pushed the branch here. Now it's as simple as a nf-core modules update busco/busco