Fix tests

[weaglesBio]

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 lint).
• Ensure the test suite passes (nextflow run . -profile 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]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @weaglesBio,

It looks like this pull-request is has been made against the sanger-tol/treeval master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the sanger-tol/treeval dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[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 e8b74e7

+| ✅ 220 tests passed       |+
#| ❔  33 tests were ignored |#
!| ❗   9 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 methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
• 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

❔ 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
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting.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: sanger_test_full.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: branch.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 2025-07-25 15:39:28