AUTHORS
CHANGES.rst
CONTRIBUTING.rst
LICENSE
LICENSE.md
MANIFEST.in
Makefile
README.md
setup.py
choppy/__init__.py
choppy/check_utils.py
choppy/choppy_pipe.py
choppy/exceptions.py
choppy/exit_code.py
choppy/utils.py
choppy/version.py
choppy/config/__init__.py
choppy/config/choppy-server.conf.example
choppy/config/choppy.conf.example
choppy/config/config.py
choppy/config/schema.py
choppy/config/schemas/config_email.json
choppy/config/schemas/config_general.json
choppy/config/schemas/config_local.json
choppy/config/schemas/config_oss.json
choppy/config/schemas/config_remote.json
choppy/config/schemas/config_repo.json
choppy/config/schemas/config_server.json
choppy/config/schemas/samples.py
choppy/core/__init__.py
choppy/core/app_utils.py
choppy/core/choppy_store.py
choppy/core/cromwell.py
choppy/core/json_checker.py
choppy/core/models.py
choppy/core/monitor.py
choppy/core/oss.py
choppy/core/project_revision.py
choppy/core/scaffold.py
choppy/core/validator.py
choppy/core/workflow.py
choppy/notification/__init__.py
choppy/notification/email_notification.py
choppy/notification/messenger.py
choppy/resources/__init__.py
choppy/resources/cromwell-configfile.template
choppy/resources/cromwell-systemd.template
choppy/resources/dockerfile-shiny.template
choppy/resources/dockerfile.template
choppy/resources/email.template
choppy/resources/mkdocs.yml.template
choppy/resources/multi_wrapper.template
choppy/resources/wrapper.template
choppy/resources/lib/ossutil64
choppy/resources/lib/ossutilmac64
choppy/resources/scaffold_template/README.md
choppy/resources/scaffold_template/defaults
choppy/resources/scaffold_template/inputs
choppy/resources/scaffold_template/workflow.wdl
choppy/resources/scaffold_template/docker/README.md
choppy/resources/scaffold_template/docker/my_program_1/Dockerfile
choppy/resources/scaffold_template/docker/my_program_1/README.md
choppy/resources/scaffold_template/docker/my_program_2/Dockerfile
choppy/resources/scaffold_template/docker/my_program_2/README.md
choppy/resources/scaffold_template/report/defaults
choppy/resources/scaffold_template/report/index.md
choppy/resources/scaffold_template/report/about/app.md
choppy/resources/scaffold_template/report/about/app_store.md
choppy/resources/scaffold_template/report/about/choppy.md
choppy/resources/scaffold_template/report/about/license.md
choppy/resources/scaffold_template/report/project/sample.md
choppy/resources/scaffold_template/tasks/task_example.wdl
choppy/resources/scaffold_template/test/README.md
choppy/resources/scaffold_template/test/samples
choppy/resources/shiny-plugin/README.md
choppy/resources/shiny-plugin/packrat.R
choppy/resources/shiny-plugin/shiny-server.sh
choppy_pipe.egg-info/PKG-INFO
choppy_pipe.egg-info/SOURCES.txt
choppy_pipe.egg-info/dependency_links.txt
choppy_pipe.egg-info/entry_points.txt
choppy_pipe.egg-info/not-zip-safe
choppy_pipe.egg-info/requires.txt
choppy_pipe.egg-info/top_level.txt
conda.recipe/bld.bat
conda.recipe/build.sh
conda.recipe/meta.yaml
docs/Makefile
docs/changelog.rst
docs/conf.py
docs/contents.rst.inc
docs/contributing.rst
docs/flaskstyle.sty
docs/index.rst
docs/installation.rst
docs/license.rst
docs/quickstart.rst
docs/requirements.txt
docs/upgrading.rst
docs/_static/choppy-icon.png
docs/_static/choppy-logo-sidebar.png
docs/_static/choppy-logo.png
docs/_static/debugger.png
docs/_static/no.png
docs/_static/pocoo.css
docs/_static/yes.png
scripts/make-release.py
tests/__init__.py
tests/config/__init__.py
tests/config/test_config.py
tests/config/test_schema.py
tests/core/__init__.py
tests/core/test_cromwell.py
tests/core/test_monitor.py
tests/core/test_parse_outputs.py
tests/core/test_queries.py
tests/examples/choppy.conf