Release 2.16.0

[d4straub]

Release 2.16.0 includes the most recent nf-core template update, dependency updates, and bug fixes.

Failing conda tests seem to have two issues:

• Default tests are running with 25.04.0 which doesnt work with conda as expected, see https://github.com/nextflow-io/nextflow/issues/5947 -> solution: increase minimum required nextflow version
• Conda/Mamba with DADA2 1.34.0 and R 4.4.3 makes trouble (the corresponding container works), see Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '...../dada2.so'  benjjneb/dada2#2094

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/ampliseq 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).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6707199

+| ✅ 364 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗ 101 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• local_component_structure - cutadapt_summary_merge.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_inseq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_in.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_quality.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - barrnapsummary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - cutadapt_summary.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_err.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_taxonomy.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_sintax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_extract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults_sintax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_barplot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sbdiexport.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_indbaligned.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_alpha.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_rmchimera.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - rename_raw_data_files.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - phyloseq_inasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - phyloseq_intax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_classify.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_filttax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - novaseq_err.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_qiime.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - trunclen.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_beta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_denoising.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancom_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - merge_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults_kraken2.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_ssu.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_intree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - combine_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_trim.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - itsx_cutasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_train.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_pplacetax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - phyloseq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_filtersamples.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_tablefiltertaxa.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_merge.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - barrnap.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export_relasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_treerecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_addspecies.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - metadata_all.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_len.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_adonis.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_fastainput.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - assignsh.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_inasv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_indb.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_alphararefaction.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_dbrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export_reltax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_filtntrim.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_betaord.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - summary_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_tree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxonomy_sidle.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_tablerecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export_absolute.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_seqrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_clusters.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_intax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_splitregions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_dbfilt.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancom_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_dbextract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - picrust.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sidle_taxrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_featuretable_group.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - format_taxresults.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - sbdiexportreannotate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_diversity_core.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - metadata_pairwise.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - treesummarizedexperiment.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_codons.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - dada2_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_seqfiltertable.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_export.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_diversity.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - cutadapt_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - robject_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_barplotavg.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - dada2_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_taxonomy.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - parse_input.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - kraken2_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - dada2_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_ancom.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - sidle_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - sintax_taxonomy_wf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - qiime2_preptax.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• nextflow_config - Config default ignored: params.report_template
• nextflow_config - Config default ignored: params.report_css
• nextflow_config - Config default ignored: params.report_logo
• files_unchanged - File ignored due to lint config: .gitattributes

✅ 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-ampliseq_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-ampliseq_logo_light.png
• files_exist - File found: docs/images/nf-core-ampliseq_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: 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-ampliseq_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/WorkflowAmpliseq.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 does not contain dev for release: 2.16.0
• 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.quality_type= Auto
• nextflow_config - Config default value correct: params.extension= /*_R{1,2}_001.fastq.gz
• nextflow_config - Config default value correct: params.min_read_counts= 1
• nextflow_config - Config default value correct: params.cutadapt_min_overlap= 3
• nextflow_config - Config default value correct: params.cutadapt_max_error_rate= 0.1
• nextflow_config - Config default value correct: params.truncq= 2
• nextflow_config - Config default value correct: params.trunc_qmin= 25
• nextflow_config - Config default value correct: params.trunc_rmin= 0.75
• nextflow_config - Config default value correct: params.max_ee= 2
• nextflow_config - Config default value correct: params.min_len= 50
• nextflow_config - Config default value correct: params.sample_inference= independent
• nextflow_config - Config default value correct: params.mergepairs_strategy= merge
• nextflow_config - Config default value correct: params.mergepairs_consensus_match= 1
• nextflow_config - Config default value correct: params.mergepairs_consensus_mismatch= -2
• nextflow_config - Config default value correct: params.mergepairs_consensus_gap= -4
• nextflow_config - Config default value correct: params.mergepairs_consensus_minoverlap= 12
• nextflow_config - Config default value correct: params.mergepairs_consensus_maxmismatch= 0
• nextflow_config - Config default value correct: params.mergepairs_consensus_percentile_cutoff= 0.001
• nextflow_config - Config default value correct: params.vsearch_cluster_id= 0.97
• nextflow_config - Config default value correct: params.raise_filter_stacksize= true
• nextflow_config - Config default value correct: params.orf_start= 1
• nextflow_config - Config default value correct: params.stop_codons= TAA,TAG
• nextflow_config - Config default value correct: params.dada_ref_taxonomy= silva=138.2
• nextflow_config - Config default value correct: params.dada_min_boot= 50
• nextflow_config - Config default value correct: params.dada_assign_chunksize= 10000
• nextflow_config - Config default value correct: params.pplace_alnmethod= hmmer
• nextflow_config - Config default value correct: params.kraken2_confidence= 0.0
• nextflow_config - Config default value correct: params.cut_its= none
• nextflow_config - Config default value correct: params.its_partial= 0
• nextflow_config - Config default value correct: params.sidle_ref_degenerates= 5
• nextflow_config - Config default value correct: params.exclude_taxa= mitochondria,chloroplast
• nextflow_config - Config default value correct: params.min_frequency= 1
• nextflow_config - Config default value correct: params.min_samples= 1
• nextflow_config - Config default value correct: params.diversity_rarefaction_depth= 500
• nextflow_config - Config default value correct: params.tax_agglom_min= 2
• nextflow_config - Config default value correct: params.tax_agglom_max= 6
• nextflow_config - Config default value correct: params.ancom_sample_min_count= 1
• nextflow_config - Config default value correct: params.ancombc_effect_size= 1.0
• nextflow_config - Config default value correct: params.ancombc_significance= 0.05
• nextflow_config - Config default value correct: params.report_title= Summary of analysis results
• nextflow_config - Config default value correct: params.seed= 100
• 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/
• 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
• nf_test_content - 'tests/failed.nf.test' contains outdir parameter
• nf_test_content - 'tests/failed.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/failed.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pacbio_its.nf.test' contains outdir parameter
• nf_test_content - 'tests/pacbio_its.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pacbio_its.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/fasta.nf.test' contains outdir parameter
• nf_test_content - 'tests/fasta.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/fasta.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sintax.nf.test' contains outdir parameter
• nf_test_content - 'tests/sintax.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sintax.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace.nf.test' contains outdir parameter
• nf_test_content - 'tests/pplace.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace.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/multi.nf.test' contains outdir parameter
• nf_test_content - 'tests/multi.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multi.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/qiimecustom.nf.test' contains outdir parameter
• nf_test_content - 'tests/qiimecustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/qiimecustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/single.nf.test' contains outdir parameter
• nf_test_content - 'tests/single.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/single.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/reftaxcustom.nf.test' contains outdir parameter
• nf_test_content - 'tests/reftaxcustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/reftaxcustom.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/novaseq.nf.test' contains outdir parameter
• nf_test_content - 'tests/novaseq.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/novaseq.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multiregion.nf.test' contains outdir parameter
• nf_test_content - 'tests/multiregion.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/multiregion.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/iontorrent.nf.test' contains outdir parameter
• nf_test_content - 'tests/iontorrent.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/iontorrent.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/doubleprimers.nf.test' contains outdir parameter
• nf_test_content - 'tests/doubleprimers.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/doubleprimers.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 - .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-ampliseq_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-ampliseq_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-ampliseq_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_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/tsv'
• 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: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting_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: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: branch.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.
• modules_config - conf/modules.config found and not ignored.
• modules_config - RENAME_RAW_DATA_FILES found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_BASIC found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_READTHROUGH found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_DOUBLEPRIMER found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - CUTADAPT_SUMMARY_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_QUALITY1 found in conf/modules.config and Nextflow scripts.
• modules_config - TRUNCLEN found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_FILTNTRIM found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_QUALITY2 found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_ERR found in conf/modules.config and Nextflow scripts.
• modules_config - NOVASEQ_ERR found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_DENOISING found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_RMCHIMERA found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_SPLITREGIONS found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_DBFILT found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_DBEXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TRIM found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_DBRECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TABLERECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TAXRECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_FILTTAX found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_SEQRECON found in conf/modules.config and Nextflow scripts.
• modules_config - SIDLE_TREERECON found in conf/modules.config and Nextflow scripts.
• modules_config - BARRNAP found in conf/modules.config and Nextflow scripts.
• modules_config - BARRNAPSUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_SSU found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_LEN_ASV found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_CODONS found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_STATS_STD found in conf/modules.config and Nextflow scripts.
• modules_config - ITSX_CUTASV found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_LEN_ITSX found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - DADA2_ADDSPECIES found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY_SINTAX found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_SINTAX found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXRESULTS_SINTAX found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXRESULTS_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_USEARCHGLOBAL found in conf/modules.config and Nextflow scripts.
• modules_config - VSEARCH_CLUSTER found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_CLUSTERS found in conf/modules.config and Nextflow scripts.
• modules_config - ASSIGNSH found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY_QIIME found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_EXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMBUILD found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_UNALIGNREF found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMALIGNREF found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_HMMALIGNQUERY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_MASK found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_MASKQUERY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_MASKREF found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_AFAFORMATQUERY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMER_AFAFORMATREF found in conf/modules.config and Nextflow scripts.
• modules_config - MAFFT found in conf/modules.config and Nextflow scripts.
• modules_config - EPANG_PLACE found in conf/modules.config and Nextflow scripts.
• modules_config - GAPPA_GRAFT found in conf/modules.config and Nextflow scripts.
• modules_config - GAPPA_ASSIGN found in conf/modules.config and Nextflow scripts.
• modules_config - GAPPA_HEATTREE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_INASV found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_PPLACETAX found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_INASV_BPAVG found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_TABLEFILTERTAXA found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_BARPLOT found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_BPAVG found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_EXPORT_ABSOLUTE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_EXPORT_RELASV found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_TREE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_FILTERSAMPLES_ANCOM found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ALPHARAREFACTION found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_DIVERSITY_CORE found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_DIVERSITY_ADONIS found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ANCOM_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - QIIME2_ANCOMBC_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - ANCOMBC_FORMULA_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - PICRUST found in conf/modules.config and Nextflow scripts.
• modules_config - SBDIEXPORT found in conf/modules.config and Nextflow scripts.
• modules_config - SBDIEXPORTREANNOTATE found in conf/modules.config and Nextflow scripts.
• modules_config - PHYLOSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - TREESUMMARIZEDEXPERIMENT found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - SUMMARY_REPORT 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: 3.5.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
• version_consistency - Version tags are consistent: manifest.version = 2.16.0, nfcore_yml.version = 2.16.0
• included_configs - Pipeline config includes custom configs.

Run details

• nf-core/tools version 3.5.1
• Run at 2025-12-19 07:26:27

[erikrikarddaniel]

Looks good. Just a question, why did you remove workflow.trace.succeeded().size() from the tests -- wasn't it stable?