.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.rst
pyproject.toml
.github/workflows/test.yml
alto/__init__.py
alto/__main__.py
alto/altocumulus.egg-info/PKG-INFO
alto/altocumulus.egg-info/SOURCES.txt
alto/altocumulus.egg-info/dependency_links.txt
alto/altocumulus.egg-info/entry_points.txt
alto/altocumulus.egg-info/not-zip-safe
alto/altocumulus.egg-info/requires.txt
alto/altocumulus.egg-info/top_level.txt
alto/commands/__init__.py
alto/commands/parse_monitoring_log.py
alto/commands/upload.py
alto/commands/cromwell/__init__.py
alto/commands/cromwell/abort.py
alto/commands/cromwell/check_status.py
alto/commands/cromwell/get_logs.py
alto/commands/cromwell/get_metadata.py
alto/commands/cromwell/list_jobs.py
alto/commands/cromwell/run.py
alto/commands/terra/__init__.py
alto/commands/terra/add_method.py
alto/commands/terra/remove_method.py
alto/commands/terra/run.py
alto/commands/terra/storage_estimate.py
alto/tests/inputs/echo.wdl
alto/tests/inputs/test_sample/test_sample_S1_L001_I1_001.fastq.gz
alto/tests/inputs/test_sample/test_sample_S1_L001_R1_001.fastq.gz
alto/tests/inputs/test_sample/test_sample_S1_L001_R2_001.fastq.gz
alto/utils/__init__.py
alto/utils/bcl_utils.py
alto/utils/dockstore_utils.py
alto/utils/fastq_utils.py
alto/utils/firecloud_utils.py
alto/utils/io_utils.py
docs/Makefile
docs/conf.py
docs/index.rst
docs/installation.rst
docs/release_notes.rst
docs/requirements.txt
docs/usage.rst
docs/_static/custom.css