.gitignore
LICENSE
README.rst
pyproject.toml
requirements.txt
setup.py
alto/__init__.py
alto/__main__.py
alto/commands/__init__.py
alto/commands/parse_monitoring_log.py
alto/commands/query.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/__init__.py
alto/tests/command_tests.py
alto/tests/test.json
alto/tests/inputs/echo.wdl
alto/tests/inputs/flowcell1/s1/s1_I1.fastq.gz
alto/tests/inputs/flowcell1/s1/s1_R1.fastq.gz
alto/tests/inputs/flowcell1/s1/s1_R2.fastq.gz
alto/tests/inputs/flowcell1/s2/s2_I1.fastq.gz
alto/tests/inputs/flowcell1/s2/s2_R1.fastq.gz
alto/tests/inputs/flowcell1/s2/s2_R2.fastq.gz
alto/tests/inputs/flowcell2/s1/s1_I1.fastq.gz
alto/tests/inputs/flowcell2/s1/s1_R1.fastq.gz
alto/tests/inputs/flowcell2/s1/s1_R2.fastq.gz
alto/tests/inputs/flowcell2/s2/s2_I1.fastq.gz
alto/tests/inputs/flowcell2/s2/s2_R1.fastq.gz
alto/tests/inputs/flowcell2/s2/s2_R2.fastq.gz
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
altocumulus.egg-info/PKG-INFO
altocumulus.egg-info/SOURCES.txt
altocumulus.egg-info/dependency_links.txt
altocumulus.egg-info/entry_points.txt
altocumulus.egg-info/not-zip-safe
altocumulus.egg-info/requires.txt
altocumulus.egg-info/top_level.txt
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