Fixes ahead of 1.4.1 release.

[weaglesBio]

• Removed unneeded def from main workflow
• Replaced ref_yahs with reference_tuple in hic_mapping

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
• 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).

[sanger-tolsoft]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f53141d

+| ✅ 219 tests passed       |+
#| ❔  33 tests were ignored |#
!| ❗  11 tests had warnings |!

Details

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 1.4.0
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
• pipeline_todos - TODO string in base.config: Check the defaults for all 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!
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
• system_exit - System.exit in treeval.nf: System.exit(1) [line 103]
• system_exit - System.exit in treeval.nf: System.exit(1) [line 110]

❔ Tests ignored:

• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• 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: assets/nf-core-treeval_logo_light.png
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
• files_exist - File is ignored: CODE_OF_CONDUCT.md
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• 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 ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.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.yml
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File ignored due to lint config: assets/nf-core-treeval_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-treeval_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-treeval_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/treeval/treeval/.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: .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/.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/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: conf/modules.config
• files_exist - File found: conf/test.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: nf-test.config
• files_exist - File found: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: conf/base.config
• 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-treeval_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/WorkflowTreeval.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: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: validation.help.enabled
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable found: validation.help.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 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.juicer= false
• nextflow_config - Config default value correct: params.binfile= false
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• 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/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 - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - assets/email_template.html 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
• readme - README Nextflow minimum version badge matched config. Badge: 24.04.4, Config: 24.04.4
• readme - README nf-core template version badge found.
• 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: 'application/x-yaml'
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: sanger_test_full.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: nf-test.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.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_MERGE found in conf/base.config and Nextflow scripts.
• base_config - BEDTOOLS_SORT found in conf/base.config and Nextflow scripts.
• base_config - SELFCOMP_ALIGNMENTBLOCKS found in conf/base.config and Nextflow scripts.
• base_config - MUMMER found in conf/base.config and Nextflow scripts.
• base_config - UCSC_BEDGRAPHTOBIGWIG found in conf/base.config and Nextflow scripts.
• base_config - CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT found in conf/base.config and Nextflow scripts.
• base_config - CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT found in conf/base.config and Nextflow scripts.
• base_config - SNAPSHOT_SRES found in conf/base.config and Nextflow scripts.
• base_config - PRETEXTMAP_STANDRD found in conf/base.config and Nextflow scripts.
• base_config - PRETEXTMAP_HIGHRES found in conf/base.config and Nextflow scripts.
• base_config - PRETEXT_GRAPH found in conf/base.config and Nextflow scripts.
• base_config - JUICER_TOOLS_PRE found in conf/base.config and Nextflow scripts.
• base_config - BWAMEM2_INDEX found in conf/base.config and Nextflow scripts.
• base_config - MINIMAP2_INDEX found in conf/base.config and Nextflow scripts.
• base_config - BAMTOBED_SORT found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_MARKDUP found in conf/base.config and Nextflow scripts.
• base_config - COOLER_CLOAD found in conf/base.config and Nextflow scripts.
• base_config - MERQURYFK_MERQURYFK found in conf/base.config and Nextflow scripts.
• base_config - BUSCO_BUSCO found in conf/base.config and Nextflow scripts.
• base_config - BUSCO_BUSCO found in conf/base.config and Nextflow scripts.
• base_config - FASTK_FASTK found in conf/base.config and Nextflow scripts.
• base_config - UCSC_BEDTOBIGBED found in conf/base.config and Nextflow scripts.
• base_config - TABIX_BGZIPTABIX found in conf/base.config and Nextflow scripts.
• base_config - GAWK_GAP_LENGTH found in conf/base.config and Nextflow scripts.
• base_config - GET_PAIRED_CONTACT_BED found in conf/base.config and Nextflow scripts.
• base_config - WINDOWMASKER_MKCOUNTS found in conf/base.config and Nextflow scripts.
• base_config - WINDOWMASKER_USTAT found in conf/base.config and Nextflow scripts.
• base_config - BEDTOOLS_INTERSECT found in conf/base.config and Nextflow scripts.
• base_config - GENERATE_CRAM_CSV found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• modules_config - GENERATE_GENOME found in conf/modules.config and Nextflow scripts.
• modules_config - PAF2BED found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_REFORMAT_INTERSECT found in conf/modules.config and Nextflow scripts.
• modules_config - MERQURYFK_MERQURYFK found in conf/modules.config and Nextflow scripts.
• modules_config - FASTK_FASTK found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_UPPER_SEQUENCE found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_CLEAN_TELOMERE found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_MAP_TELO found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_GAP_LENGTH found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_REPLACE_DOTS found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_RENAME_IDS found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_REFORMAT_INTERSECT found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_EXTRACT_BUSCOGENE found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - GNU_SORT_A found in conf/modules.config and Nextflow scripts.
• modules_config - GNU_SORT_B found in conf/modules.config and Nextflow scripts.
• modules_config - GNU_SORT_C found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_MAKEWINDOWS found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_INTERSECT found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_MAP found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_CUTN found in conf/modules.config and Nextflow scripts.
• modules_config - MINIPROT_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SPLIT_REF found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SPLIT_QUERY found in conf/modules.config and Nextflow scripts.
• modules_config - FIND_TELOMERE_REGIONS found in conf/modules.config and Nextflow scripts.
• modules_config - FIND_TELOMERE_WINDOWS found in conf/modules.config and Nextflow scripts.
• modules_config - BUSCO_BUSCO found in conf/modules.config and Nextflow scripts.
• modules_config - PRETEXTMAP_STANDRD found in conf/modules.config and Nextflow scripts.
• modules_config - PRETEXTMAP_HIGHRES found in conf/modules.config and Nextflow scripts.
• modules_config - PRETEXT_INGEST_SNDRD found in conf/modules.config and Nextflow scripts.
• modules_config - PRETEXT_INGEST_HIRES found in conf/modules.config and Nextflow scripts.
• modules_config - YAHS found in conf/modules.config and Nextflow scripts.
• modules_config - SNAPSHOT_SRES found in conf/modules.config and Nextflow scripts.
• modules_config - JUICER_TOOLS_PRE found in conf/modules.config and Nextflow scripts.
• modules_config - COOLER_CLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - MERQURYFK_MERQURYFK 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: 3.3.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.3.1
• Run at 2025-08-22 10:23:29