Improve overall stats, fix test_filter issue

[erikrikarddaniel]

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/metatdenovo branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core 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).

This started out to deal with the test_filter problem plus fixing a number of linting warnings regarding how local modules and subworkflows are organized, but turned into an overhaul of the overall stats table. Linting warnings not addressed yet.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a64ae1d

+| ✅ 237 tests passed       |+
!| ❗  26 tests had warnings |!

❗ Test warnings:

• system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]
• schema_description - Ungrouped param in schema: validationSkipDuplicateCheck
• schema_description - Ungrouped param in schema: validationS3PathCheck
• local_component_structure - sum_eukulele_taxonomy.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - collect_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - prokkagff2tsv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - unpigz.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - transrate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sum_kofamscan.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - formatspades.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - writespadesyaml.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_prodigal.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_diamond_tax_ranklist.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_eukulele_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - hmmrank.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_diamond_tax_taxdump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - collect_featurecounts.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - transdecoder.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - merge_summary_tables.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - eggnog.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prodigal.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prokka_subsets.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - fastqc_trimgalore.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - kofamscan.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - hmmclassify.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - eukulele.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ 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-metatdenovo_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-metatdenovo_logo_light.png
• files_exist - File found: docs/images/nf-core-metatdenovo_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: conf/igenomes_ignored.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-metatdenovo_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/WorkflowMetatdenovo.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: 1.1dev
• 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.outdir= ./results
• nextflow_config - Config default value correct: params.bbnorm_target= 100
• nextflow_config - Config default value correct: params.bbnorm_min= 5
• nextflow_config - Config default value correct: params.user_assembly_name= user_assembly
• nextflow_config - Config default value correct: params.min_contig_length= 0
• nextflow_config - Config default value correct: params.spades_flavor= rna
• nextflow_config - Config default value correct: params.bbmap_minid= 0.9
• nextflow_config - Config default value correct: params.user_orfs_name= user_orfs
• nextflow_config - Config default value correct: params.prokka_batchsize= 10 MB
• nextflow_config - Config default value correct: params.eggnog_dbpath= eggnog
• nextflow_config - Config default value correct: params.kofam_dir= ./kofam/
• nextflow_config - Config default value correct: params.hmmpattern= *.hmm
• nextflow_config - Config default value correct: params.diamond_top= 10
• nextflow_config - Config default value correct: params.eukulele_method= mets
• nextflow_config - Config default value correct: params.eukulele_dbpath= ./eukulele/
• 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-metatdenovo_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-metatdenovo_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-metatdenovo_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: 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
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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
• 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.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_MERGEPE found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_BBNORM found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
• modules_config - MEGAHIT_INTERLEAVED found in conf/modules.config and Nextflow scripts.
• modules_config - WRITESPADESYAML found in conf/modules.config and Nextflow scripts.
• modules_config - SPADES found in conf/modules.config and Nextflow scripts.
• modules_config - FORMATSPADES found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_SEQ_CONTIG_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - PRODIGAL found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_PRODIGAL_GFF found in conf/modules.config and Nextflow scripts.
• modules_config - TRANSDECODER found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
• modules_config - FAA_CAT found in conf/modules.config and Nextflow scripts.
• modules_config - FFN_CAT found in conf/modules.config and Nextflow scripts.
• modules_config - GFF_CAT found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKAGFF2TSV found in conf/modules.config and Nextflow scripts.
• modules_config - COLLECT_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - HMMRANK found in conf/modules.config and Nextflow scripts.
• modules_config - EGGNOG_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - EGGNOG_MAPPER found in conf/modules.config and Nextflow scripts.
• modules_config - KOFAMSCAN_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - KOFAMSCAN_SCAN found in conf/modules.config and Nextflow scripts.
• modules_config - EUKULELE_SEARCH found in conf/modules.config and Nextflow scripts.
• modules_config - DIAMOND_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - TAXONKIT_LINEAGE found in conf/modules.config and Nextflow scripts.
• modules_config - PIGZ_DIAMOND_LINEAGE found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_DIAMOND_TAX_RANKLIST found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_DIAMOND_TAX_TAXDUMP found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_EUKULELE_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - SUM_EUKULELE_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - COLLECT_STATS 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: 3.2.0

Run details

• nf-core/tools version 3.2.0
• Run at 2025-02-01 22:36:27

[danilodileo]

LGTM

[danilodileo]

Are you taking care of issues #324 #322 #313 with this PR?

[erikrikarddaniel]

Are you taking care of issues #324 #322 #313 with this PR?

Mostly #322. I had the intention of dealing with #324 but ran out of time and #313 is probably done before, at least to some extent. I'll close #322 and #313 now.