[ljwharbers]

Summary

Puts .github/workflows/claude-review.yml and REVIEW.md on main. The files are byte-identical to the ones in #208 (into dev).

GitHub only runs issue_comment workflows from the default branch, so the @claude review comment trigger does nothing until the workflow is on main. That trigger is the only way to review fork PRs. The automatic review on same-repo PRs already works from dev via #208.

Only these two files change. The CHANGELOG entry stays in #208. Because the files are identical on both branches, the next dev → main release merges cleanly.

Notes

• This PR comes from the patch branch, which branch.yml accepts for PRs into main.
• Main-only workflows such as download_pipeline run on this PR. Their known failures (cramino stub, HKU wget) are unrelated to this change.
• This PR is not a draft, so opening it should trigger the first automatic Claude review, run from this PR's copy of the workflow. Use it to check that inline comments and a summary get posted.

🤖 Generated with Claude Code

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8ad23f0

+| ✅ 204 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  39 tests had warnings |!

Details

❗ Test warnings:

• 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 README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• 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 meta.yml: #Add a description of the module and list keywords
• 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 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• 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 - deepsomatic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - small_variant_consensus.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 - prepare_annotation.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
• 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= clair
• nextflow_config - Config default value correct: params.somatic_var_keep= 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= clair
• nextflow_config - Config default value correct: params.prioritize_caller_somatic= clair
• 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/consensus.nf.test' contains outdir parameter
• nf_test_content - 'tests/consensus.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/deep_only.nf.test' contains outdir parameter
• nf_test_content - 'tests/deep_only.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/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: linting_comment.yml
• actions_schema_validation - Workflow validation passed: branch.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: clean-up.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: linting.yml
• actions_schema_validation - Workflow validation passed: claude-review.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 2026-09-29 14:17:12