Release 2.10.0

[d4straub]

This release contains a few updates to the reference taxonomy databases, nf-core template update 2.14.1, better differential abundance analysis tools, and some bug fixes. For details please check the CHANGELOG!

Besides reviews, before merging I will confirm that:

• the new parameter section on the website is fine
• the AWS test succeeds

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 lint).
• Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
• 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 lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a1511ef

+| ✅ 284 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 2.10.0
• readme - README did not have a Nextflow minimum version badge.

❔ 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
• actions_ci - actions_ci

✅ 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-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: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File 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 - 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: params.validationShowHiddenParams
• nextflow_config - Config variable found: params.validationSchemaIgnoreParams
• 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 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 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.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.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.vsearch_cluster_id= 0.97
• 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
• 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.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.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• 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
• 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_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 Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (347 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: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - QIIME2_EXTRACT found in conf/base.config and Nextflow scripts.
• 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 - 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: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-06-27 07:33:32

[jannikseidelQBiC]

LGTM! Just minor visual complaints (harshil alignment in some of the local modules and subworkflows), but I leave it to you to decide if this should be changed. Well done!

[erikrikarddaniel]

👍

[d4straub]

Thanks for the reviews!