Remove vulnerable PR-comment artifact pattern

[mashehu]

Security patch

This PR applies a security fix included in nf-core/tools 4.0.3 for a potential exploit in the GitHub Actions workflows that post comments on pull requests.

For details, see the related security advisory: https://nf-co.re/advisories/pr-comment-workflow-vulnerability

The fix must be merged into the default branch to take effect. Please merge this PR as soon as possible.

These changes only affect CI workflows, so merging them into the default branch does not require a new pipeline release.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f079c45

+| ✅ 388 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗ 108 tests had warnings |!

Details

❗ Test warnings:

• pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/ampliseq/ampliseq/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
  _
• local_component_structure - qiime2_filtersamples.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 - format_taxresults_sintax.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_samples.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 - qiime2_ancombc2_tax.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - cutadapt_summary_merge.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_qiime.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 - treesummarizedexperiment.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 - barrnapsummary.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 - qiime2_intax.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 - itsx_cutasv.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 - sidle_tablerecon.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 - format_taxresults_vsearch_lca.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 - format_taxresults_kraken2.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 - format_taxonomy_vsearch_lca.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 - dada2_rmchimera.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 - trunclen.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 - qiime2_barplot.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_seqfiltertable.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 - dada2_quality.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 - qiime2_ancombc_asv.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 - phyloseq.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 - sbdiexport.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 - dada2_splitregions.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_in.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 - sidle_trim.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_denoising.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_train.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 - filter_sequences_abundances.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 - metadata_all.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 - qiime2_export_relasv.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 - sidle_dbfilt.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_dbrecon.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - qiime2_ancombc2_asv.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 - dada2_filtntrim.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 - sidle_dbextract.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 - qiime2_classify.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_alphararefaction.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_ancom_asv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - decontam.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 - filter_ssu.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_tree.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - download_reference.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 - itsxrust_cutasv.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 - qiime2_diversity_adonis.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 - qiime2_tablefiltertaxa.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 - filter_len.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 - format_taxonomy.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 - sidle_indbaligned.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 - cutadapt_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 - parse_input.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 - qiime2_taxonomy.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - vsearch_lca_taxonomy_wf.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 - qiime2_export.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 - qiime2_preptax.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 - kraken2_taxonomy_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 - robject_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: .github/workflows/linting_comment.yml
• 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
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File does not exist: .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/nf-core-ampliseq_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ampliseq_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-ampliseq_logo_dark.png
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ 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/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.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/CONTRIBUTING.md
• 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: 2.18.0
• 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.decontam= none
• nextflow_config - Config default value correct: params.decontam_decontaminate_method= auto
• nextflow_config - Config default value correct: params.decontam_decontaminate_threshold= 0.1
• nextflow_config - Config default value correct: params.decontam_notcontaminant_threshold= 0.5
• 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= sbdi-gtdb=R11-RS232-1
• 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= clustalo
• nextflow_config - Config default value correct: params.kraken2_confidence= 0.0
• nextflow_config - Config default value correct: params.vsearch_lca_id= 0.9
• nextflow_config - Config default value correct: params.vsearch_lca_maxaccepts= 0
• nextflow_config - Config default value correct: params.vsearch_lca_maxrejects= 0
• nextflow_config - Config default value correct: params.vsearch_lca_lca_cutoff= 0.9
• nextflow_config - Config default value correct: params.vsearch_lca_query_cov= 1.0
• 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.its_extractor= itsx
• 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.run_pplace= false
• 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/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/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/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/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/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/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/vsearch_lca.nf.test' contains outdir parameter
• nf_test_content - 'tests/vsearch_lca.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/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/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/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/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/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/pplace_sheet.nf.test' contains outdir parameter
• nf_test_content - 'tests/pplace_sheet.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pplace_sheet.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/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/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/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 - 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 - docs/README.md 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: 25.10.4, Config: 25.10.4
• readme - README nf-core template version badge found.
• 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/tsv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• 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
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: pr-comment.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: download_pipeline.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - DOWNLOAD_REFERENCE found in conf/modules.config and Nextflow scripts.
• 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 - 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 - DECONTAM 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 - ITSXRUST_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_USEARCHGLOBAL_LCA found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXONOMY_VSEARCH_LCA found in conf/modules.config and Nextflow scripts.
• modules_config - FORMAT_TAXRESULTS_VSEARCH_LCA 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_HMMRANK 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 - CLUSTALO_ALIGN 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 - PPLACEFORMATTAX 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_ALPHA 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 - QIIME2_ANCOMBC2_TAX found in conf/modules.config and Nextflow scripts.
• modules_config - ANCOMBC2_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: 4.0.2
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
• container_configs - conf/containers_conda_lock_files_amd64.config is up to date
• container_configs - conf/containers_conda_lock_files_arm64.config is up to date
• container_configs - conf/containers_docker_amd64.config is up to date
• container_configs - conf/containers_docker_arm64.config is up to date
• container_configs - conf/containers_singularity_https_amd64.config is up to date
• container_configs - conf/containers_singularity_https_arm64.config is up to date
• container_configs - conf/containers_singularity_oras_amd64.config is up to date
• container_configs - conf/containers_singularity_oras_arm64.config is up to date
• version_consistency - Version tags are consistent: manifest.version = 2.18.0, nfcore_yml.version = 2.18.0
• included_configs - Pipeline config includes custom configs.

Run details

• nf-core/tools version 4.0.2
• Run at 2026-07-24 13:31:03

[github-actions]

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

• ❌ singularity | latest-everything | Shard 11/16

See the full run for details.