LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
nf_core/.pre-commit-prettier-config.yaml
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nf_core/__main__.py
nf_core/bump_version.py
nf_core/create.py
nf_core/download.py
nf_core/launch.py
nf_core/licences.py
nf_core/lint_utils.py
nf_core/list.py
nf_core/refgenie.py
nf_core/schema.py
nf_core/sync.py
nf_core/utils.py
nf_core.egg-info/PKG-INFO
nf_core.egg-info/SOURCES.txt
nf_core.egg-info/dependency_links.txt
nf_core.egg-info/entry_points.txt
nf_core.egg-info/not-zip-safe
nf_core.egg-info/requires.txt
nf_core.egg-info/top_level.txt
nf_core/components/__init__.py
nf_core/components/components_command.py
nf_core/components/components_create.py
nf_core/components/components_test.py
nf_core/components/components_utils.py
nf_core/components/info.py
nf_core/components/install.py
nf_core/components/list.py
nf_core/components/remove.py
nf_core/components/update.py
nf_core/lint/__init__.py
nf_core/lint/actions_awsfulltest.py
nf_core/lint/actions_awstest.py
nf_core/lint/actions_ci.py
nf_core/lint/actions_schema_validation.py
nf_core/lint/files_exist.py
nf_core/lint/files_unchanged.py
nf_core/lint/merge_markers.py
nf_core/lint/modules_json.py
nf_core/lint/modules_structure.py
nf_core/lint/multiqc_config.py
nf_core/lint/nextflow_config.py
nf_core/lint/pipeline_name_conventions.py
nf_core/lint/pipeline_todos.py
nf_core/lint/readme.py
nf_core/lint/schema_description.py
nf_core/lint/schema_lint.py
nf_core/lint/schema_params.py
nf_core/lint/template_strings.py
nf_core/lint/version_consistency.py
nf_core/module-template/modules/main.nf
nf_core/module-template/modules/meta.yml
nf_core/module-template/tests/main.nf
nf_core/module-template/tests/nextflow.config
nf_core/module-template/tests/test.yml
nf_core/modules/__init__.py
nf_core/modules/bump_versions.py
nf_core/modules/create.py
nf_core/modules/info.py
nf_core/modules/install.py
nf_core/modules/list.py
nf_core/modules/modules_differ.py
nf_core/modules/modules_json.py
nf_core/modules/modules_repo.py
nf_core/modules/modules_test.py
nf_core/modules/modules_utils.py
nf_core/modules/mulled.py
nf_core/modules/nfcore_module.py
nf_core/modules/patch.py
nf_core/modules/remove.py
nf_core/modules/test_yml_builder.py
nf_core/modules/update.py
nf_core/modules/lint/__init__.py
nf_core/modules/lint/main_nf.py
nf_core/modules/lint/meta_yml.py
nf_core/modules/lint/module_changes.py
nf_core/modules/lint/module_deprecations.py
nf_core/modules/lint/module_patch.py
nf_core/modules/lint/module_tests.py
nf_core/modules/lint/module_todos.py
nf_core/modules/lint/module_version.py
nf_core/pipeline-template/.editorconfig
nf_core/pipeline-template/.gitattributes
nf_core/pipeline-template/.gitignore
nf_core/pipeline-template/.gitpod.yml
nf_core/pipeline-template/.nf-core.yml
nf_core/pipeline-template/.prettierignore
nf_core/pipeline-template/.prettierrc.yml
nf_core/pipeline-template/CHANGELOG.md
nf_core/pipeline-template/CITATIONS.md
nf_core/pipeline-template/CODE_OF_CONDUCT.md
nf_core/pipeline-template/LICENSE
nf_core/pipeline-template/README.md
nf_core/pipeline-template/main.nf
nf_core/pipeline-template/modules.json
nf_core/pipeline-template/nextflow.config
nf_core/pipeline-template/nextflow_schema.json
nf_core/pipeline-template/pyproject.toml
nf_core/pipeline-template/.devcontainer/devcontainer.json
nf_core/pipeline-template/.github/.dockstore.yml
nf_core/pipeline-template/.github/CONTRIBUTING.md
nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
nf_core/pipeline-template/.github/ISSUE_TEMPLATE/config.yml
nf_core/pipeline-template/.github/ISSUE_TEMPLATE/feature_request.yml
nf_core/pipeline-template/.github/workflows/awsfulltest.yml
nf_core/pipeline-template/.github/workflows/awstest.yml
nf_core/pipeline-template/.github/workflows/branch.yml
nf_core/pipeline-template/.github/workflows/ci.yml
nf_core/pipeline-template/.github/workflows/fix-linting.yml
nf_core/pipeline-template/.github/workflows/linting.yml
nf_core/pipeline-template/.github/workflows/linting_comment.yml
nf_core/pipeline-template/assets/adaptivecard.json
nf_core/pipeline-template/assets/email_template.html
nf_core/pipeline-template/assets/email_template.txt
nf_core/pipeline-template/assets/methods_description_template.yml
nf_core/pipeline-template/assets/multiqc_config.yml
nf_core/pipeline-template/assets/samplesheet.csv
nf_core/pipeline-template/assets/schema_input.json
nf_core/pipeline-template/assets/sendmail_template.txt
nf_core/pipeline-template/assets/slackreport.json
nf_core/pipeline-template/bin/check_samplesheet.py
nf_core/pipeline-template/conf/base.config
nf_core/pipeline-template/conf/igenomes.config
nf_core/pipeline-template/conf/modules.config
nf_core/pipeline-template/conf/test.config
nf_core/pipeline-template/conf/test_full.config
nf_core/pipeline-template/docs/README.md
nf_core/pipeline-template/docs/output.md
nf_core/pipeline-template/docs/usage.md
nf_core/pipeline-template/docs/images/mqc_fastqc_adapter.png
nf_core/pipeline-template/docs/images/mqc_fastqc_counts.png
nf_core/pipeline-template/docs/images/mqc_fastqc_quality.png
nf_core/pipeline-template/lib/NfcoreSchema.groovy
nf_core/pipeline-template/lib/NfcoreTemplate.groovy
nf_core/pipeline-template/lib/Utils.groovy
nf_core/pipeline-template/lib/WorkflowMain.groovy
nf_core/pipeline-template/lib/WorkflowPipeline.groovy
nf_core/pipeline-template/lib/nfcore_external_java_deps.jar
nf_core/pipeline-template/modules/local/samplesheet_check.nf
nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml
nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml
nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
nf_core/pipeline-template/subworkflows/local/input_check.nf
nf_core/pipeline-template/workflows/pipeline.nf
nf_core/subworkflow-template/subworkflows/main.nf
nf_core/subworkflow-template/subworkflows/meta.yml
nf_core/subworkflow-template/tests/main.nf
nf_core/subworkflow-template/tests/nextflow.config
nf_core/subworkflow-template/tests/test.yml
nf_core/subworkflows/__init__.py
nf_core/subworkflows/create.py
nf_core/subworkflows/info.py
nf_core/subworkflows/install.py
nf_core/subworkflows/list.py
nf_core/subworkflows/remove.py
nf_core/subworkflows/subworkflows_test.py
nf_core/subworkflows/test_yml_builder.py
nf_core/subworkflows/update.py
tests/__init__.py
tests/test_bump_version.py
tests/test_cli.py
tests/test_create.py
tests/test_download.py
tests/test_launch.py
tests/test_licenses.py
tests/test_lint.py
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tests/lint/__init__.py
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