Update to 1.2.0

[DarianHole]

Adding in changes to 1.2.0

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!
• 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 3f2b5a3

+| ✅ 180 tests passed       |+
#| ❔  52 tests were ignored |#
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• 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!
• included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File is ignored: .github/CONTRIBUTING.md
• files_exist - File is ignored: .github/.dockstore.yml
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: conf/test.config
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: assets/email_template.txt
• files_exist - File is ignored: assets/email_template.html
• files_exist - File is ignored: assets/sendmail_template.txt
• files_exist - File is ignored: assets/adaptivecard.json
• files_exist - File is ignored: assets/slackreport.json
• files_exist - File is ignored: assets/nf-core-measeq_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-measeq_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-measeq_logo_dark.png
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: assets/multiqc_config.yml
• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: ro-crate-metadata.json
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: process.cpus
• nextflow_config - Config variable ignored: process.memory
• nextflow_config - Config variable ignored: process.time
• nextflow_config - Config variable ignored: validation.help.beforeText
• nextflow_config - Config variable ignored: validation.help.afterText
• nextflow_config - Config variable ignored: validation.summary.beforeText
• nextflow_config - Config variable ignored: validation.summary.afterText
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File does not exist: .github/.dockstore.yml
• files_unchanged - File does not exist: .github/CONTRIBUTING.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File does not exist: assets/email_template.html
• files_unchanged - File does not exist: assets/email_template.txt
• files_unchanged - File does not exist: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-measeq_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-measeq_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-measeq_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/measeq/measeq/.github/workflows/awstest.yml
• multiqc_config - multiqc_config

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/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: conf/modules.config
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: main.nf
• files_exist - File found: conf/base.config
• 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-measeq_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/WorkflowMeaseq.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: validation.help.enabled
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable found: validation.help.command
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version does not contain dev for release: 1.2.0
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.ivar_trim_min_read_length= 30
• nextflow_config - Config default value correct: params.ivar_offset= 0
• nextflow_config - Config default value correct: params.min_ambiguity_threshold= 0.3
• nextflow_config - Config default value correct: params.max_ambiguity_threshold= 0.75
• nextflow_config - Config default value correct: params.min_indel_threshold= 0.6
• nextflow_config - Config default value correct: params.min_alt_fraction_freebayes= 0.05
• nextflow_config - Config default value correct: params.min_variant_qual_freebayes= 20
• nextflow_config - Config default value correct: params.align_bowtie2= false
• nextflow_config - Config default value correct: params.ont_min_read_length= 200
• nextflow_config - Config default value correct: params.ont_min_base_qual= 12
• nextflow_config - Config default value correct: params.normalise_ont= 500
• nextflow_config - Config default value correct: params.ont_keep_incorrect_primers= false
• nextflow_config - Config default value correct: params.min_variant_qual_c3= 7
• nextflow_config - Config default value correct: params.min_allele_freq_c3= 0.6
• nextflow_config - Config default value correct: params.min_mask_freq_c3= 0.3
• nextflow_config - Config default value correct: params.min_site_threshold_c3= 0.05
• nextflow_config - Config default value correct: params.min_depth= 10
• nextflow_config - Config default value correct: params.neg_control_pct_threshold= 10
• nextflow_config - Config default value correct: params.neg_ctrl_substrings= neg,ntc,blank,en
• nextflow_config - Config default value correct: params.nextclade_dataset_name= nextstrain/measles/N450/WHO-2012
• nextflow_config - Config default value correct: params.nextclade_dataset_tag= 2025-03-26--11-47-13Z
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.validate_params= true
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: ci_workflow.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - NANOQ found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP found in conf/modules.config and Nextflow scripts.
• modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_CONSENSUS_AMBIGUOUS found in conf/modules.config and Nextflow scripts.
• modules_config - NEXTCLADE_DATASETGET found in conf/modules.config and Nextflow scripts.
• modules_config - NEXTCLADE_RUN_N450 found in conf/modules.config and Nextflow scripts.
• modules_config - NEXTCLADE_RUN_CUSTOM found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_COVERAGE found in conf/modules.config and Nextflow scripts.
• modules_config - QUAST found in conf/modules.config and Nextflow scripts.
• modules_config - CALCULATE_BAM_VARIATION found in conf/modules.config and Nextflow scripts.
• modules_config - STAGE_FILE_IRIDANEXT found in conf/modules.config and Nextflow scripts.
• modules_config - GENERATE_REF_INTERMEDIATES found in conf/modules.config and Nextflow scripts.
• modules_config - GENERATE_AMPLICON_BED found in conf/modules.config and Nextflow scripts.
• modules_config - SPLIT_AMPLICON_REGION found in conf/modules.config and Nextflow scripts.
• modules_config - PREDICT_GENOTYPE found in conf/modules.config and Nextflow scripts.
• modules_config - BWAMEM2_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
• modules_config - IVAR_TRIM found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
• modules_config - PROCESS_VCF found in conf/modules.config and Nextflow scripts.
• modules_config - ARTIC_GET_MODELS found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - ALIGN_TRIM found in conf/modules.config and Nextflow scripts.
• modules_config - CLAIR3 found in conf/modules.config and Nextflow scripts.
• modules_config - ARTIC_VCF_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_VCF_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
• modules_config - VCF_TO_TSV found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_CONSENSUS found in conf/modules.config and Nextflow scripts.
• modules_config - ADJUST found in conf/modules.config and Nextflow scripts.
• modules_config - COMPARE_INTERNAL_DSID found in conf/modules.config and Nextflow scripts.
• modules_config - MAKE_SAMPLE_QC_CSV found in conf/modules.config and Nextflow scripts.
• modules_config - MAKE_FINAL_QC_CSV found in conf/modules.config and Nextflow scripts.
• modules_config - SAMPLE_AMPLICON found in conf/modules.config and Nextflow scripts.
• modules_config - AMPLICON_ found in conf/modules.config and Nextflow scripts.
• modules_config - AMPLICON_MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - POSITIONAL_N_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - PYSAMSTATS found in conf/modules.config and Nextflow scripts.
• modules_config - NORMALIZE_DEPTH_MATRIX found in conf/modules.config and Nextflow scripts.
• modules_config - MAKE_CUSTOM_REPORT found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.2.1
• version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

• nf-core/tools version 3.2.1
• Run at 2026-05-20 13:50:33