MANIFEST.in
Makefile
README.rst
cwltool.py
gittaggers.py
requirements.txt
setup.cfg
setup.py
test-requirements.txt
cwltool/__init__.py
cwltool/__main__.py
cwltool/argparser.py
cwltool/builder.py
cwltool/checker.py
cwltool/command_line_tool.py
cwltool/context.py
cwltool/cwlNodeEngine.js
cwltool/cwlNodeEngineJSConsole.js
cwltool/cwlNodeEngineWithContext.js
cwltool/cwlrdf.py
cwltool/docker.py
cwltool/docker_id.py
cwltool/draft2tool.py
cwltool/errors.py
cwltool/executors.py
cwltool/expression.py
cwltool/extensions.yml
cwltool/factory.py
cwltool/flatten.py
cwltool/job.py
cwltool/load_tool.py
cwltool/loghandler.py
cwltool/main.py
cwltool/mutation.py
cwltool/pack.py
cwltool/pathmapper.py
cwltool/process.py
cwltool/provenance.py
cwltool/resolver.py
cwltool/sandboxjs.py
cwltool/secrets.py
cwltool/singularity.py
cwltool/software_requirements.py
cwltool/stdfsaccess.py
cwltool/update.py
cwltool/utils.py
cwltool/validate_js.py
cwltool/workflow.py
cwltool.egg-info/PKG-INFO
cwltool.egg-info/SOURCES.txt
cwltool.egg-info/dependency_links.txt
cwltool.egg-info/entry_points.txt
cwltool.egg-info/requires.txt
cwltool.egg-info/top_level.txt
cwltool.egg-info/zip-safe
cwltool/jshint/jshint.js
cwltool/jshint/jshint_wrapper.js
cwltool/schemas/draft-2/CommonWorkflowLanguage.yml
cwltool/schemas/draft-2/cwl-avro.yml
cwltool/schemas/draft-3/CommandLineTool-standalone.yml
cwltool/schemas/draft-3/CommandLineTool.yml
cwltool/schemas/draft-3/CommonWorkflowLanguage.yml
cwltool/schemas/draft-3/Process.yml
cwltool/schemas/draft-3/README.md
cwltool/schemas/draft-3/UserGuide.yml
cwltool/schemas/draft-3/Workflow.yml
cwltool/schemas/draft-3/concepts.md
cwltool/schemas/draft-3/contrib.md
cwltool/schemas/draft-3/index.yml
cwltool/schemas/draft-3/intro.md
cwltool/schemas/draft-3/invocation.md
cwltool/schemas/draft-3/userguide-intro.md
cwltool/schemas/draft-3/salad/schema_salad/metaschema/field_name.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/field_name_proc.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/field_name_schema.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/field_name_src.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/ident_res.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/ident_res_proc.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/ident_res_schema.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/ident_res_src.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/import_include.md
cwltool/schemas/draft-3/salad/schema_salad/metaschema/link_res.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/link_res_proc.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/link_res_schema.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/link_res_src.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/metaschema.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/salad.md
cwltool/schemas/draft-3/salad/schema_salad/metaschema/vocab_res.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/vocab_res_proc.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/vocab_res_schema.yml
cwltool/schemas/draft-3/salad/schema_salad/metaschema/vocab_res_src.yml
cwltool/schemas/v1.0/CommandLineTool-standalone.yml
cwltool/schemas/v1.0/CommandLineTool.yml
cwltool/schemas/v1.0/CommonWorkflowLanguage.yml
cwltool/schemas/v1.0/Process.yml
cwltool/schemas/v1.0/README.md
cwltool/schemas/v1.0/UserGuide.yml
cwltool/schemas/v1.0/Workflow.yml
cwltool/schemas/v1.0/concepts.md
cwltool/schemas/v1.0/contrib.md
cwltool/schemas/v1.0/intro.md
cwltool/schemas/v1.0/invocation.md
cwltool/schemas/v1.0/userguide-intro.md
cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_proc.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_schema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_src.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_proc.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_schema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_src.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md
cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res_proc.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res_schema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res_src.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res_proc.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res_schema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/map_res_src.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/metaschema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/metaschema_base.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md
cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res_proc.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res_schema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/typedsl_res_src.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/vocab_res.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/vocab_res_proc.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/vocab_res_schema.yml
cwltool/schemas/v1.0/salad/schema_salad/metaschema/vocab_res_src.yml
cwltool/schemas/v1.1.0-dev1/CommandLineTool-standalone.yml
cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml
cwltool/schemas/v1.1.0-dev1/CommonWorkflowLanguage.yml
cwltool/schemas/v1.1.0-dev1/Process.yml
cwltool/schemas/v1.1.0-dev1/README.md
cwltool/schemas/v1.1.0-dev1/UserGuide.yml
cwltool/schemas/v1.1.0-dev1/Workflow.yml
cwltool/schemas/v1.1.0-dev1/concepts.md
cwltool/schemas/v1.1.0-dev1/contrib.md
cwltool/schemas/v1.1.0-dev1/intro.md
cwltool/schemas/v1.1.0-dev1/invocation.md
cwltool/schemas/v1.1.0-dev1/userguide-intro.md
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/field_name.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/field_name_proc.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/field_name_schema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/field_name_src.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_proc.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_schema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res_src.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res_proc.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res_schema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res_src.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/map_res.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/map_res_proc.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/map_res_schema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/map_res_src.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/metaschema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/metaschema_base.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/typedsl_res.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/typedsl_res_proc.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/typedsl_res_schema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/typedsl_res_src.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_proc.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_schema.yml
cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/vocab_res_src.yml
tests/2.fasta
tests/2.fastq
tests/__init__.py
tests/echo-cwlrun-job.yaml
tests/echo-job.yaml
tests/echo.cwl
tests/echo_broken_outputs.cwl
tests/listing-job.yml
tests/non_portable.cwl
tests/non_portable2.cwl
tests/portable.cwl
tests/random_lines.cwl
tests/random_lines_job.json
tests/random_lines_mapping.cwl
tests/seqtk_seq.cwl
tests/seqtk_seq_job.json
tests/seqtk_seq_with_docker.cwl
tests/seqtk_seq_wrong_name.cwl
tests/test_bad_outputs_wf.cwl
tests/test_check.py
tests/test_cwl_version.py
tests/test_default_path.py
tests/test_deps_env_resolvers_conf.yml
tests/test_deps_env_resolvers_conf_rewrite.yml
tests/test_deps_mapping.yml
tests/test_docker_warning.py
tests/test_examples.py
tests/test_ext.py
tests/test_fetch.py
tests/test_http_input.py
tests/test_iwdr.py
tests/test_js_sandbox.py
tests/test_override.py
tests/test_pack.py
tests/test_parallel.py
tests/test_pathmapper.py
tests/test_provenance.py
tests/test_rdfprint.py
tests/test_relax_path_checks.py
tests/test_secrets.py
tests/test_toolargparse.py
tests/test_validate_js.py
tests/utf_doc_example.cwl
tests/util.py
tests/checker_wf/broken-wf.cwl
tests/checker_wf/broken-wf2.cwl
tests/checker_wf/cat.cwl
tests/checker_wf/echo.cwl
tests/checker_wf/functional-wf.cwl
tests/override/echo-job-ov.yml
tests/override/echo-job-ov2.yml
tests/override/echo-job.yml
tests/override/echo-wf.cwl
tests/override/echo.cwl
tests/override/ov.yml
tests/override/ov2.yml
tests/override/ov3.yml
tests/tmp1/tmp2/tmp3/.gitkeep
tests/wf/1st-workflow.cwl
tests/wf/arguments.cwl
tests/wf/badout1.cwl
tests/wf/badout2.cwl
tests/wf/badout3.cwl
tests/wf/cache_test_workflow.cwl
tests/wf/cat-tool.cwl
tests/wf/cat.cwl
tests/wf/count-lines1-wf.cwl
tests/wf/default-dir5.cwl
tests/wf/default-wf5.cwl
tests/wf/default_path.cwl
tests/wf/echo.cwl
tests/wf/empty.ttl
tests/wf/expect_packed.cwl
tests/wf/formattest-job.json
tests/wf/formattest.cwl
tests/wf/hello-workflow.cwl
tests/wf/hello.txt
tests/wf/hello_single_tool.cwl
tests/wf/iwdr-entry.cwl
tests/wf/js_output.cwl
tests/wf/js_output_workflow.cwl
tests/wf/listing_deep.cwl
tests/wf/listing_none.cwl
tests/wf/listing_shallow.cwl
tests/wf/listing_v1_0.cwl
tests/wf/malformed_outputs.cwl
tests/wf/missing_cwlVersion.cwl
tests/wf/mut.cwl
tests/wf/mut2.cwl
tests/wf/mut3.cwl
tests/wf/nested.cwl
tests/wf/networkaccess-fail.cwl
tests/wf/networkaccess.cwl
tests/wf/parseInt-tool.cwl
tests/wf/revsort-job.json
tests/wf/revsort.cwl
tests/wf/revtool.cwl
tests/wf/scatter-job2.json
tests/wf/scatter-wf4.cwl
tests/wf/scatterfail.cwl
tests/wf/sec-tool.cwl
tests/wf/sec-wf.cwl
tests/wf/secret_job.cwl
tests/wf/secret_wf.cwl
tests/wf/separate_without_prefix.cwl
tests/wf/sorttool.cwl
tests/wf/tar-param.cwl
tests/wf/timelimit-fail.cwl
tests/wf/timelimit.cwl
tests/wf/touch_tool.cwl
tests/wf/trick_defaults.cwl
tests/wf/updatedir.cwl
tests/wf/updatedir_inplace.cwl
tests/wf/updateval.cwl
tests/wf/updateval.py
tests/wf/updateval_inplace.cwl
tests/wf/vf-concat.cwl
tests/wf/wc-job.json
tests/wf/wc-tool.cwl
tests/wf/wffail.cwl
tests/wf/whale.txt
tests/wf/workreuse-fail.cwl
tests/wf/workreuse.cwl
tests/wf/wrong_cwlVersion.cwl