feat(pipelines): migrate lint rules to AST-grep

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Create a pipeline and test it on: pull_request

RunTestWorkflow (25.10.4)

RunTestWorkflow (latest-everything)

Python tests on: pull_request 8

Get test file matrix

Run test_datasets/test_test_datasets_search.py with Python 3.10 and Nextflow 25.10.4

Run test_datasets/test_test_datasets_utils.py with Python 3.10 and Nextflow 25.10.4

Run test_cli.py with Python 3.10 and Nextflow 25.10.4

Run test_components.py with Python 3.10 and Nextflow 25.10.4

Run test_lint_utils.py with Python 3.10 and Nextflow 25.10.4

Run test_test_utils.py with Python 3.10 and Nextflow 25.10.4

Run test_modules.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_modules_json.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_bump_versions.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_list.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_update.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_containers.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_modules_utils.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_create.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_patch.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_info.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_install.py with Python 3.10 and Nextflow 25.10.4

Run modules/test_remove.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_todos.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_deprecations.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_lint_utils.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_changes.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_meta_yml.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_containers.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_lint_local.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_version.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_lint_integration.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_tests.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_main_nf.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_module_lint_remotes.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_patch.py with Python 3.10 and Nextflow 25.10.4

Run modules/lint/test_environment_yml.py with Python 3.10 and Nextflow 25.10.4

Run components/test_completion.py with Python 3.10 and Nextflow 25.10.4

Run components/test_components_snapshot_test.py with Python 3.10 and Nextflow 25.10.4

Run components/test_components_generate_snapshot.py with Python 3.10 and Nextflow 25.10.4

Run components/test_components_utils.py with Python 3.10 and Nextflow 25.10.4

Run test_utils.py with Python 3.10 and Nextflow 25.10.4

Run test_pipelines.py with Python 3.10 and Nextflow 25.10.4

Run test_astgrep.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_refgenie.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/download/test_container.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/download/test_docker.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/download/test_download.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/download/test_utils.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/download/test_singularity.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_create_logo.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_lint.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_list.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_completion.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_launch.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_bump_version.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_params_file.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_rocrate.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_create.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_sync.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_create_app.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_container_configs.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/test_schema.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_files_exist.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_nf_test_content.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_configs.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_modules_json.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_actions_awsfulltest.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_nfcore_yml.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_merge_markers.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_version_consistency.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_astgrep_rules.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_actions_schema_validation.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_actions_awstest.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_plugin_includes.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_nextflow_config.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_files_unchanged.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_template_strings.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_local_component_structure.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_rocrate_readme_sync.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_if_empty_null.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_container_configs.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_actions_nf_test.py with Python 3.10 and Nextflow 25.10.4

Run pipelines/lint/test_multiqc_config.py with Python 3.10 and Nextflow 25.10.4

Run test_subworkflows.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_list.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_update.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_create.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_patch.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_info.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_install.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/test_remove.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/lint/test_integration.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/lint/test_nf_test.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/lint/test_local.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/lint/test_main_nf.py with Python 3.10 and Nextflow 25.10.4

Run subworkflows/lint/test_patch.py with Python 3.10 and Nextflow 25.10.4

Lint tools code formatting on: pull_request

pre-commit

Create a pipeline from a template and test it on: pull_request

Retrieve all template features

RunTestWorkflow (github_badges)

RunTestWorkflow (changelog)

RunTestWorkflow (license)

RunTestWorkflow (ci)

RunTestWorkflow (nf-test)

RunTestWorkflow (igenomes)

RunTestWorkflow (modules)

RunTestWorkflow (multiqc)

RunTestWorkflow (fastqc)

RunTestWorkflow (nf_schema)

RunTestWorkflow (nf_core_configs)

RunTestWorkflow (seqera_platform)

RunTestWorkflow (gpu)

RunTestWorkflow (codespaces)

RunTestWorkflow (vscode)

RunTestWorkflow (code_linters)

RunTestWorkflow (citations)

RunTestWorkflow (documentation)

RunTestWorkflow (rocrate)

RunTestWorkflow (email)

RunTestWorkflow (all)

Create a pipeline and run nf-core linting on: pull_request

MakeTestWorkflow (25.10.4)

MakeTestWorkflow (latest-everything)

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