.coveragerc
.flake8
.gitmodules
.pyre_configuration
.readthedocs.yml
CONTRIBUTING.md
Dockerfile
LICENSE
Makefile
README.md
requirements.dev.txt
requirements.txt
setup.cfg
setup.py
.github/pull_request_template.md
.github/workflows/CI.yml
WDL/CLI.py
WDL/Env.py
WDL/Error.py
WDL/Expr.py
WDL/Lint.py
WDL/StdLib.py
WDL/Tree.py
WDL/Type.py
WDL/Value.py
WDL/Walker.py
WDL/__init__.py
WDL/__main__.py
WDL/_error_util.py
WDL/_grammar.py
WDL/_parser.py
WDL/_util.py
WDL/runtime/__init__.py
WDL/runtime/_statusbar.py
WDL/runtime/cache.py
WDL/runtime/config.py
WDL/runtime/download.py
WDL/runtime/error.py
WDL/runtime/task.py
WDL/runtime/task_container.py
WDL/runtime/workflow.py
WDL/runtime/config_templates/default.cfg
docs/FAQ.md
docs/Makefile
docs/WDL.rst
docs/add_functions.md
docs/assert.md
docs/check.rst
docs/conf.py
docs/getting_started.md
docs/index.rst
docs/miniwdl-logo.png
docs/runner_advanced.md
docs/runner_cli.rst
docs/runner_reference.md
docs/trace_identifiers.md
docs/wdlviz.md
docs/wdlviz_ex1.png
docs/wdlviz_ex2.png
examples/clean_download_cache.sh
examples/clean_download_cache.t
examples/paste_wdl_imports.py
examples/run_with_custom_error.py
examples/upload_output_files.sh
examples/wdlviz.py
examples/plugin_log_task_usage/miniwdl_log_task_usage.py
examples/plugin_log_task_usage/setup.py
examples/plugin_s3_progressive_upload/miniwdl_s3_progressive_upload.py
examples/plugin_s3_progressive_upload/setup.py
examples/plugin_task_omnibus/miniwdl_task_omnibus_example.py
examples/plugin_task_omnibus/setup.py
miniwdl.egg-info/PKG-INFO
miniwdl.egg-info/SOURCES.txt
miniwdl.egg-info/dependency_links.txt
miniwdl.egg-info/entry_points.txt
miniwdl.egg-info/not-zip-safe
miniwdl.egg-info/pbr.json
miniwdl.egg-info/requires.txt
miniwdl.egg-info/top_level.txt
stubs/README.md
stubs/argcomplete/__init__.py
stubs/bullet/__init__.py
stubs/coloredlogs/__init__.py
stubs/docker/__init__.py
stubs/importlib_metadata/__init__.py
stubs/lark/__init__.py
stubs/lark/exceptions.py
stubs/psutil/__init__.py
stubs/pygtail/__init__.py
stubs/pythonjsonlogger/jsonlogger.py
stubs/regex/__init__.py
stubs/ruamel/yaml.py
stubs/xdg/__init__.py
test_corpi/README.md
test_corpi/DataBiosphere/topmed-workflows
test_corpi/ENCODE-DCC/atac-seq-pipeline
test_corpi/ENCODE-DCC/chip-seq-pipeline2
test_corpi/ENCODE-DCC/rna-seq-pipeline
test_corpi/ENCODE-DCC/wgbs-pipeline
test_corpi/HumanCellAtlas/skylab
test_corpi/biowdl/aligning
test_corpi/biowdl/expression-quantification
test_corpi/biowdl/small-rna
test_corpi/biowdl/somatic-variantcalling
test_corpi/biowdl/tasks
test_corpi/broadinstitute/gtex-pipeline
test_corpi/broadinstitute/viral-ngs
test_corpi/broadinstitute/warp
test_corpi/contrived/check_quant.wdl
test_corpi/contrived/contrived.wdl
test_corpi/contrived/emptier.wdl
test_corpi/contrived/empty.wdl
test_corpi/contrived/incomplete.wdl
test_corpi/contrived/incomplete_call.wdl
test_corpi/contrived/incomplete_import.wdl
test_corpi/contrived/issue120.wdl
test_corpi/contrived/issue81.wdl
test_corpi/contrived/issue82.wdl
test_corpi/contrived/scatter_collisions.wdl
test_corpi/contrived/tricky_outputs.wdl
test_corpi/contrived/unverified_struct.wdl
test_corpi/contrived/wdl1.1.wdl
test_corpi/dnanexus/dxWDL
test_corpi/gatk-workflows/broad-prod-wgs-germline-snps-indels
test_corpi/gatk-workflows/five-dollar-genome-analysis-pipeline
test_corpi/gatk-workflows/gatk4-cnn-variant-filter
test_corpi/gatk-workflows/gatk4-germline-snps-indels
test_corpi/gatk-workflows/gatk4-somatic-snvs-indels
tests/__init__.py
tests/alyssa_ben.txt
tests/bash-tap
tests/check.t
tests/context.py
tests/no_docker_services.py
tests/runner.t
tests/test_0eval.py
tests/test_1doc.py
tests/test_2calls.py
tests/test_3corpi.py
tests/test_4taskrun.py
tests/test_5stdlib.py
tests/test_6workflowrun.py
tests/test_7runner.py
tests/test_8cache.py
tests/test_cli_argcomplete.py
tests/applied/DVGLx.t
tests/applied/SARS-CoV-2.t
tests/applied/encode_atac_seq.t
tests/applied/getting_started.t
tests/applied/skylab.py
tests/applied/skylab_bulk_rna.t
tests/applied/viral_assemble.t
tests/applied/viral_refbased.t
tools_image/Dockerfile
tools_image/README.md