Fix defaults

[robert-a-forsyth]

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).

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[github-actions]

This PR is against the main 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 @robert-a-forsyth,

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

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 85adfe7

+| ✅ 203 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  39 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/lrsomatic/lrsomatic/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
  _
• schema_description - Ungrouped param in schema: skip_modkit
• schema_description - No description provided in schema for parameter: generate_gvcf
• schema_description - No description provided in schema for parameter: autocorrelation
• schema_description - No description provided in schema for parameter: vep_custom
• schema_description - No description provided in schema for parameter: vep_custom_tbi
• schema_description - No description provided in schema for parameter: severus_minsupport
• schema_description - No description provided in schema for parameter: wakhan_chroms
• local_component_structure - small_variant_consensus.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - deepsomatic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_reference_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - phasing_haplotyping.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-lrsomatic_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_dark.png
• 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: .github/CONTRIBUTING.md
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.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_comment.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/nf-core-lrsomatic_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/lrsomatic/lrsomatic/.github/workflows/awstest.yml

✅ 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/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: conf/test_full.config
• files_exist - File found: docs/CONTRIBUTING.md
• 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.config
• files_exist - File found: conf/igenomes_ignored.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-lrsomatic_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/WorkflowLrsomatic.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: 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 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: 1.1.0
• 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.germline_var_keep= deepvariant,clair
• nextflow_config - Config default value correct: params.somatic_var_keep= deepsomatic,clair
• nextflow_config - Config default value correct: params.germline_var_combine= all
• nextflow_config - Config default value correct: params.somatic_var_combine= all
• nextflow_config - Config default value correct: params.prioritize_caller_germline= deepvariant
• nextflow_config - Config default value correct: params.prioritize_caller_somatic= deepsomatic
• nextflow_config - Config default value correct: params.longphase_tag_supplementary= false
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.save_secondary_alignment= true
• nextflow_config - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/
• nextflow_config - Config default value correct: params.vep_args= --everything --filter_common --per_gene --total_length --offline --format vcf
• nextflow_config - Config default value correct: params.vep_cache_version= 113
• nextflow_config - Config default value correct: params.severus_minsupport= 3
• nextflow_config - Config default value correct: params.ascat_penalty= 150
• nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
• nextflow_config - Config default value correct: params.ascat_min_counts= 10
• nextflow_config - Config default value correct: params.ascat_min_map_qual= 10
• nextflow_config - Config default value correct: params.ascat_longread_bins= 2000
• nextflow_config - Config default value correct: params.ascat_allelecounter_flags= -f 0
• 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.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/
• nf_test_content - 'tests/clair_only.nf.test' contains outdir parameter
• nf_test_content - 'tests/clair_only.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/deep_only.nf.test' contains outdir parameter
• nf_test_content - 'tests/deep_only.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/consensus.nf.test' contains outdir parameter
• nf_test_content - 'tests/consensus.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/union.nf.test' contains outdir parameter
• nf_test_content - 'tests/union.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 - LICENSE matches the template
• files_unchanged - .github/.dockstore.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 - assets/email_template.html matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore 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: 25.04.0, Config: 25.04.0
• readme - README nf-core template version badge found.
• 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: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.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
• 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 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - ENSEMBLVEP_DOWNLOAD 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 = 1.1.0, nfcore_yml.version = 1.1.0

Run details

• nf-core/tools version 4.0.2
• Run at 2026-06-01 11:16:45