Index

Symbols

--add-ga4gh-tool-registry cwltool command line option --basedir cwltool command line option --cachedir cwltool command line option --cidfile-dir cwltool command line option --cidfile-prefix cwltool command line option --compute-checksum cwltool command line option --copy-outputs cwltool command line option --custom-net cwltool command line option --debug cwltool command line option --default-container cwltool command line option --disable-color cwltool command line option --disable-ga4gh-tool-registry cwltool command line option --disable-host-provenance cwltool command line option --disable-js-validation cwltool command line option --disable-pull cwltool command line option --disable-user-provenance cwltool command line option --doc-cache cwltool command line option --enable-color cwltool command line option --enable-dev cwltool command line option --enable-ext cwltool command line option --enable-ga4gh-tool-registry cwltool command line option --enable-host-provenance cwltool command line option --enable-pull cwltool command line option --enable-user-provenance cwltool command line option --eval-timeout cwltool command line option --force-docker-pull cwltool command line option --full-name cwltool command line option --help cwltool command line option --js-console cwltool command line option --js-hint-options-file cwltool command line option --leave-container cwltool command line option --leave-outputs cwltool command line option --leave-tmpdir cwltool command line option --log-dir cwltool command line option --make-template cwltool command line option --move-outputs cwltool command line option --mpi-config-file cwltool command line option --no-compute-checksum cwltool command line option --no-container cwltool command line option --no-doc-cache cwltool command line option --no-match-user cwltool command line option --no-read-only cwltool command line option --non-strict cwltool command line option

--on-error cwltool command line option --orcid cwltool command line option --outdir cwltool command line option --overrides cwltool command line option --pack cwltool command line option --parallel cwltool command line option --podman cwltool command line option --preserve-entire-environment cwltool command line option --preserve-environment cwltool command line option --print-deps cwltool command line option --print-dot cwltool command line option --print-input-deps cwltool command line option --print-pre cwltool command line option --print-rdf cwltool command line option --print-subgraph cwltool command line option --print-supported-versions cwltool command line option --print-targets cwltool command line option --provenance cwltool command line option --quiet cwltool command line option --rdf-serializer cwltool command line option --relative-deps cwltool command line option --relax-path-checks cwltool command line option --rm-container cwltool command line option --rm-tmpdir cwltool command line option --single-process cwltool command line option --single-step cwltool command line option --singularity cwltool command line option --skip-schemas cwltool command line option --strict cwltool command line option --strict-cpu-limit cwltool command line option --strict-memory-limit cwltool command line option --target cwltool command line option --timestamps cwltool command line option --tmp-outdir-prefix cwltool command line option --tmpdir-prefix cwltool command line option --tool-help cwltool command line option --udocker cwltool command line option --user-space-docker-cmd cwltool command line option --validate cwltool command line option --verbose cwltool command line option --version cwltool command line option -h cwltool command line option -t cwltool command line option

_

__author__ (in module cwltool) __call__() (cwltool.argparser.AppendAction method) (cwltool.argparser.FSAction method) (cwltool.argparser.FSAppendAction method) (cwltool.executors.JobExecutor method) (cwltool.factory.Callable method)

__citation__ (in module cwltool.provenance_constants) __contains__() (cwltool.pathmapper.PathMapper method) __iter__() (cwltool.pathmapper.PathMapper method) __repr__() (cwltool.job.JobBase method) __str__() (cwltool.process.Process method) (cwltool.provenance.ResearchObject method) (cwltool.provenance_profile.ProvenanceProfile method)

A

abspath() (in module cwltool.stdfsaccess) AbstractOperation (class in cwltool.command_line_tool) ACCOUNT_UUID (in module cwltool.provenance_constants) activity_has_provenance() (cwltool.provenance_profile.ProvenanceProfile method) add() (cwltool.secrets.SecretStore method) (cwltool.task_queue.TaskQueue method) add_annotation() (cwltool.provenance.ResearchObject method) add_argument() (in module cwltool.argparser) add_data_file() (cwltool.provenance.ResearchObject method) add_file_or_directory_volume() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) add_sizes() (in module cwltool.process) add_tagfile() (cwltool.provenance.ResearchObject method) add_to_manifest() (cwltool.provenance.ResearchObject method) add_uri() (cwltool.provenance.ResearchObject method) add_volumes() (cwltool.job.ContainerCommandLineJob method) add_writable_directory_volume() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method)

add_writable_file_volume() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) adjustDirObjs() (in module cwltool.utils) adjustFileObjs() (in module cwltool.utils) Aggregate (in module cwltool.provenance) ALLUPDATES (in module cwltool.update) Annotation (in module cwltool.provenance) append_volume() (cwltool.docker.DockerCommandLineJob static method) (cwltool.job.ContainerCommandLineJob static method) (cwltool.singularity.SingularityCommandLineJob static method) (cwltool.udocker.UDockerCommandLineJob static method) AppendAction (class in cwltool.argparser) arg_parser() (in module cwltool.argparser) ArgumentException aslist() (in module cwltool.utils) AuthoredBy (in module cwltool.provenance) avroize_type() (in module cwltool.process)

B

bind_input() (cwltool.builder.Builder method) boot2docker_id() (in module cwltool.docker_id) boot2docker_running() (in module cwltool.docker_id)

build_job_script() (cwltool.builder.Builder method) (cwltool.software_requirements.DependenciesConfiguration method) Builder (class in cwltool.builder) bytes2str_in_dicts() (in module cwltool.utils)

C

Callable (class in cwltool.factory) CallbackJob (class in cwltool.command_line_tool) can_assign_src_to_sink() (in module cwltool.checker) check_adjust() (in module cwltool.command_line_tool) check_all_types() (in module cwltool.checker) check_format() (in module cwltool.builder) check_js_threshold_version() (in module cwltool.sandboxjs) check_output_and_strip() (in module cwltool.docker_id) check_types() (in module cwltool.checker) check_valid_locations() (in module cwltool.command_line_tool) check_working_directories() (in module cwltool.main) checkRequirements() (in module cwltool.process) checksum_copy() (in module cwltool.provenance) checkversion() (in module cwltool.update) choose_process() (in module cwltool.main) choose_step() (in module cwltool.main) choose_target() (in module cwltool.main) circular_dependency_checker() (in module cwltool.checker) cleanIntermediate() (in module cwltool.process) close() (cwltool.provenance.ResearchObject method) (cwltool.provenance.WritableBagFile method) cmd_output_matches() (in module cwltool.docker_id) cmd_output_to_int() (in module cwltool.docker_id) cmp_like_py2() (in module cwltool.utils) code_fragment_to_js() (in module cwltool.sandboxjs) collect_output() (cwltool.command_line_tool.CommandLineTool method) collect_output_ports() (cwltool.command_line_tool.CommandLineTool method) CollectOutputsType (in module cwltool.job) COMMAND_WITH_DEPENDENCIES_TEMPLATE (in module cwltool.software_requirements) CommandLineJob (class in cwltool.job) CommandLineTool (class in cwltool.command_line_tool) compute_checksums() (in module cwltool.process) configure_logging() (in module cwltool.loghandler) CONTAINER_TMPDIR (cwltool.job.ContainerCommandLineJob attribute) ContainerCommandLineJob (class in cwltool.job) CONTENT_LIMIT (in module cwltool.utils) content_limit_respected_read() (in module cwltool.builder) content_limit_respected_read_bytes() (in module cwltool.builder) ContextBase (class in cwltool.context) CONTROL_CODE_RE (in module cwltool.job) copy() (cwltool.context.LoadingContext method) (cwltool.context.RuntimeContext method) copy_job_order() (in module cwltool.provenance_profile) copytree_with_merge() (in module cwltool.utils) create_file_and_add_volume() (cwltool.job.ContainerCommandLineJob method) create_job() (cwltool.provenance.ResearchObject method) create_outdir() (cwltool.context.RuntimeContext method) create_runtime() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method) create_tmp_dir() (in module cwltool.utils) create_tmpdir() (cwltool.context.RuntimeContext method) crossproduct_size() (in module cwltool.workflow_job) cuda_check() (in module cwltool.cuda) cuda_version_and_device_count() (in module cwltool.cuda) custom_schemas (in module cwltool.process) CWL_CONTENT_TYPES (in module cwltool) cwl_document cwltool command line option cwl_files (in module cwltool.process) CWL_IANA (in module cwltool.process) CWLObjectType (in module cwltool.utils) CWLOutputAtomType (in module cwltool.utils) CWLOutputType (in module cwltool.utils) CWLPROV (in module cwltool.provenance_constants) CWLPROV_VERSION (in module cwltool.provenance_constants) cwltool module cwltool command line option --add-ga4gh-tool-registry --basedir --cachedir --cidfile-dir --cidfile-prefix --compute-checksum --copy-outputs --custom-net --debug --default-container --disable-color --disable-ga4gh-tool-registry --disable-host-provenance --disable-js-validation --disable-pull --disable-user-provenance --doc-cache --enable-color --enable-dev --enable-ext --enable-ga4gh-tool-registry --enable-host-provenance --enable-pull --enable-user-provenance --eval-timeout --force-docker-pull --full-name --help --js-console --js-hint-options-file --leave-container --leave-outputs --leave-tmpdir --log-dir --make-template --move-outputs --mpi-config-file --no-compute-checksum --no-container --no-doc-cache --no-match-user --no-read-only --non-strict --on-error --orcid --outdir --overrides --pack --parallel --podman --preserve-entire-environment --preserve-environment --print-deps --print-dot --print-input-deps --print-pre --print-rdf --print-subgraph --print-supported-versions --print-targets --provenance --quiet --rdf-serializer --relative-deps --relax-path-checks --rm-container --rm-tmpdir --single-process --single-step --singularity --skip-schemas --strict --strict-cpu-limit --strict-memory-limit --target --timestamps --tmp-outdir-prefix --tmpdir-prefix --tool-help --udocker --user-space-docker-cmd --validate --verbose --version -h -t cwl_document inputs_object

cwltool.__main__ module cwltool.argparser module cwltool.builder module cwltool.checker module cwltool.command_line_tool module cwltool.context module cwltool.cuda module cwltool.cwlrdf module cwltool.cwlviewer module cwltool.docker module cwltool.docker_id module cwltool.env_to_stdout module cwltool.errors module cwltool.executors module cwltool.expression module cwltool.factory module cwltool.flatten module cwltool.job module cwltool.load_tool module cwltool.loghandler module cwltool.main module cwltool.mpi module cwltool.mutation module cwltool.pack module cwltool.pathmapper module cwltool.process module cwltool.procgenerator module cwltool.provenance module cwltool.provenance_constants module cwltool.provenance_profile module cwltool.resolver module cwltool.run_job module cwltool.sandboxjs module cwltool.secrets module cwltool.singularity module cwltool.singularity_utils module cwltool.software_requirements module cwltool.stdfsaccess module cwltool.subgraph module cwltool.task_queue module cwltool.udocker module cwltool.update module cwltool.utils module cwltool.validate_js module cwltool.workflow module cwltool.workflow_job module CWLViewer (class in cwltool.cwlviewer)

D

DATA (in module cwltool.provenance_constants) declare_artefact() (cwltool.provenance_profile.ProvenanceProfile method) declare_directory() (cwltool.provenance_profile.ProvenanceProfile method) declare_file() (cwltool.provenance_profile.ProvenanceProfile method) declare_node() (in module cwltool.subgraph) declare_string() (cwltool.provenance_profile.ProvenanceProfile method) dedup() (in module cwltool.utils) default_loader() (in module cwltool.load_tool) default_make_tool (in module cwltool.context) (in module cwltool.workflow) default_make_tool() (in module cwltool.workflow) default_timeout (in module cwltool.sandboxjs) DEFAULT_TMP_PREFIX (in module cwltool.utils) defaultStreamHandler (in module cwltool.loghandler) DependenciesConfiguration (class in cwltool.software_requirements) deserialize_env() (in module cwltool.env_to_stdout) DestinationsType (in module cwltool.utils) DEVUPDATES (in module cwltool.update)

DirectoryAction (class in cwltool.argparser) DirectoryAppendAction (class in cwltool.argparser) DirectoryType (in module cwltool.utils) do_eval() (cwltool.builder.Builder method) (in module cwltool.expression) do_output_callback() (cwltool.workflow_job.WorkflowJob method) docker_machine_id() (in module cwltool.docker_id) docker_machine_name() (in module cwltool.docker_id) docker_machine_running() (in module cwltool.docker_id) docker_monitor() (cwltool.job.ContainerCommandLineJob method) docker_vm_id() (in module cwltool.docker_id) DockerCommandLineJob (class in cwltool.docker) dot() (cwltool.cwlviewer.CWLViewer method) dot_with_parameters() (in module cwltool.cwlrdf) dot_without_parameters() (in module cwltool.cwlrdf) dotproduct_scatter() (in module cwltool.workflow_job) DOWN (in module cwltool.subgraph) downloadHttpFile() (in module cwltool.utils) drain() (cwltool.task_queue.TaskQueue method)

E

ENCODING (in module cwltool.provenance_constants) ensure_galaxy_lib_available() (in module cwltool.software_requirements) ensure_non_writable() (in module cwltool.utils) ensure_writable() (in module cwltool.utils) eval_resource() (in module cwltool.process) evalResources() (cwltool.process.Process method) evaluate() (cwltool.provenance_profile.ProvenanceProfile method)

evaluator() (in module cwltool.expression) exec_js_process() (in module cwltool.sandboxjs) execjs() (in module cwltool.sandboxjs) execute() (cwltool.executors.JobExecutor method) (cwltool.executors.NoopJobExecutor method) exists() (cwltool.stdfsaccess.StdFsAccess method) ExpressionJob (class in cwltool.command_line_tool) ExpressionTool (class in cwltool.command_line_tool)

F

Factory (class in cwltool.factory) fcntl (in module cwltool.utils) fetch_document() (in module cwltool.load_tool) FILE_COUNT_WARNING (in module cwltool.process) FileAction (class in cwltool.argparser) FileAppendAction (class in cwltool.argparser) files() (cwltool.pathmapper.PathMapper method) fill_in_defaults() (in module cwltool.process) filter() (cwltool.process.LogAsDebugFilter method) (cwltool.validate_js.SuppressLog method) finalize_prov_profile() (cwltool.provenance_profile.ProvenanceProfile method) find_default_container() (in module cwltool.main)

find_deps() (in module cwltool.main) find_ids() (in module cwltool.pack) find_run() (in module cwltool.pack) find_step() (in module cwltool.subgraph) flat_crossproduct_scatter() (in module cwltool.workflow_job) flatten() (in module cwltool.flatten) FOAF (in module cwltool.provenance_constants) FORCE_SHELLED_POPEN (in module cwltool.job) formatSubclassOf() (in module cwltool.builder) formatTime() (cwltool.main.ProvLogFormatter method) FSAction (class in cwltool.argparser) FSAppendAction (class in cwltool.argparser)

G

ga4gh_tool_registries (in module cwltool.resolver) GA4GH_TRS_FILES (in module cwltool.resolver) GA4GH_TRS_PRIMARY_DESCRIPTOR (in module cwltool.resolver) gather() (in module cwltool.cwlrdf) generate_arg() (cwltool.builder.Builder method) generate_example_input() (in module cwltool.main) generate_input_template() (in module cwltool.main) generate_output_prov() (cwltool.provenance_profile.ProvenanceProfile method) generate_parser() (in module cwltool.argparser) generate_prov_doc() (cwltool.provenance_profile.ProvenanceProfile method) generate_snapshot() (cwltool.provenance.ResearchObject method) get_container_from_software_requirements() (in module cwltool.software_requirements) get_default_args() (in module cwltool.argparser) get_dependencies() (in module cwltool.software_requirements) get_dependency_tree() (in module cwltool.checker) get_dot_graph() (cwltool.cwlviewer.CWLViewer method) get_expressions() (in module cwltool.validate_js) get_from_requirements() (cwltool.docker.DockerCommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.singularity.SingularityCommandLineJob method)

get_image() (cwltool.docker.DockerCommandLineJob static method) (cwltool.singularity.SingularityCommandLineJob static method) get_listing() (in module cwltool.utils) get_outdir() (cwltool.context.RuntimeContext method) get_overrides() (in module cwltool.process) get_process() (in module cwltool.subgraph) get_requirement() (cwltool.utils.HasReqsHints method) get_schema() (in module cwltool.process) get_stagedir() (cwltool.context.RuntimeContext method) get_step() (in module cwltool.subgraph) get_step_id() (in module cwltool.checker) get_subgraph() (in module cwltool.subgraph) get_tmpdir() (cwltool.context.RuntimeContext method) get_version() (in module cwltool.singularity) getdefault() (in module cwltool.context) glob() (cwltool.stdfsaccess.StdFsAccess method) GraphTargetMissingException

H

handle_software_environment() (in module cwltool.run_job) has_data_file() (cwltool.provenance.ResearchObject method) has_secret() (cwltool.secrets.SecretStore method)

Hasher (in module cwltool.provenance_constants) HasReqsHints (class in cwltool.utils) have_node_slim (in module cwltool.sandboxjs)

I

identity() (in module cwltool.update) import_embed() (in module cwltool.pack) in_flight (cwltool.task_queue.TaskQueue attribute) inherit_reqshints() (in module cwltool.main) init_job_order() (in module cwltool.main) INPUT (in module cwltool.subgraph) INPUT_OBJ_VOCAB (in module cwltool.builder) inputs_object cwltool command line option INTERNAL_VERSION (in module cwltool.update)

interpolate() (in module cwltool.expression) is_apptainer_1_or_newer() (in module cwltool.singularity) is_conditional_step() (in module cwltool.checker) is_expression() (in module cwltool.validate_js) is_version_2_6() (in module cwltool.singularity) is_version_3_1_or_newer() (in module cwltool.singularity) is_version_3_4_or_newer() (in module cwltool.singularity) is_version_3_or_newer() (in module cwltool.singularity) isdir() (cwltool.stdfsaccess.StdFsAccess method) isfile() (cwltool.stdfsaccess.StdFsAccess method) items() (cwltool.pathmapper.PathMapper method)

J

JavascriptException job() (cwltool.command_line_tool.AbstractOperation method) (cwltool.command_line_tool.CommandLineTool method) (cwltool.command_line_tool.ExpressionTool method) (cwltool.process.Process method) (cwltool.procgenerator.ProcessGenerator method) (cwltool.procgenerator.ProcessGeneratorJob method) (cwltool.workflow.Workflow method) (cwltool.workflow.WorkflowStep method) (cwltool.workflow_job.WorkflowJob method) (cwltool.workflow_job.WorkflowJobStep method)

JobBase (class in cwltool.job) JobExecutor (class in cwltool.executors) jobloaderctx (in module cwltool.load_tool) JobsGeneratorType (in module cwltool.utils) JobsType (in module cwltool.utils) join() (cwltool.stdfsaccess.StdFsAccess method) (cwltool.task_queue.TaskQueue method) jshead() (in module cwltool.expression) jshint_js() (in module cwltool.validate_js) JSHintJSReturn (in module cwltool.validate_js) JSONAtomType (in module cwltool.utils) JSONType (in module cwltool.utils)

L

lastpart() (in module cwltool.cwlrdf) listdir() (cwltool.stdfsaccess.StdFsAccess method) load() (cwltool.mpi.MpiConfig class method) load_job_order() (in module cwltool.main) load_overrides() (in module cwltool.load_tool) load_tool() (in module cwltool.load_tool) loading_context (cwltool.factory.Factory attribute)

LoadingContext (class in cwltool.context) LoadRefType (in module cwltool.pack) local_path() (in module cwltool.utils) localdata (in module cwltool.sandboxjs) log_handler() (in module cwltool.context) LogAsDebugFilter (class in cwltool.process) LOGS (in module cwltool.provenance_constants)

M

MAIN (in module cwltool.provenance_constants) main() (in module cwltool.env_to_stdout) (in module cwltool.main) (in module cwltool.run_job) make() (cwltool.factory.Factory method) make_job_runner() (cwltool.command_line_tool.CommandLineTool method) make_path_mapper() (cwltool.command_line_tool.CommandLineTool method) make_relative() (in module cwltool.main) make_template() (in module cwltool.main) make_tool() (in module cwltool.load_tool) make_tool_notimpl() (in module cwltool.context) make_workflow_step() (cwltool.workflow.Workflow method) mapper() (cwltool.pathmapper.PathMapper method) MapperEnt (in module cwltool.pathmapper) match_types() (in module cwltool.workflow_job) merge_flatten_type() (in module cwltool.checker) mergedirs() (in module cwltool.process) METADATA (in module cwltool.provenance_constants) minimum_node_version_str (in module cwltool.sandboxjs) missing_subset() (in module cwltool.checker) module cwltool cwltool.__main__ cwltool.argparser cwltool.builder cwltool.checker cwltool.command_line_tool cwltool.context cwltool.cuda cwltool.cwlrdf cwltool.cwlviewer cwltool.docker cwltool.docker_id cwltool.env_to_stdout cwltool.errors cwltool.executors cwltool.expression cwltool.factory cwltool.flatten cwltool.job cwltool.load_tool cwltool.loghandler cwltool.main cwltool.mpi cwltool.mutation cwltool.pack cwltool.pathmapper cwltool.process cwltool.procgenerator cwltool.provenance cwltool.provenance_constants cwltool.provenance_profile cwltool.resolver cwltool.run_job cwltool.sandboxjs cwltool.secrets cwltool.singularity cwltool.singularity_utils cwltool.software_requirements cwltool.stdfsaccess cwltool.subgraph cwltool.task_queue cwltool.udocker cwltool.update cwltool.utils cwltool.validate_js cwltool.workflow cwltool.workflow_job

MpiConfig (class in cwltool.mpi) MpiConfigT (in module cwltool.mpi) MPIRequirementName (in module cwltool.mpi) msvcrt (in module cwltool.utils) MultithreadedJobExecutor (class in cwltool.executors) MutationManager (class in cwltool.mutation) MutationState (in module cwltool.mutation)

N

needs_parsing() (in module cwltool.expression) needs_shell_quoting_re (in module cwltool.job) nestdir() (in module cwltool.process) nested_crossproduct_scatter() (in module cwltool.workflow_job) neverquote() (in module cwltool.job)

new_js_proc() (in module cwltool.sandboxjs) next_seg() (in module cwltool.expression) Node (in module cwltool.subgraph) NoopJobExecutor (class in cwltool.executors) normalizeFilesDirs() (in module cwltool.utils)

O

objclass (cwltool.argparser.DirectoryAction attribute) (cwltool.argparser.DirectoryAppendAction attribute) (cwltool.argparser.FileAction attribute) (cwltool.argparser.FileAppendAction attribute) (cwltool.argparser.FSAction attribute) (cwltool.argparser.FSAppendAction attribute) object_from_state() (in module cwltool.workflow_job) open() (cwltool.stdfsaccess.StdFsAccess method) open_log_file_for_activity() (cwltool.provenance.ResearchObject method)

ORCID (in module cwltool.provenance_constants) ORDERED_VERSIONS (in module cwltool.update) ORE (in module cwltool.provenance_constants) ORIGINAL_CWLVERSION (in module cwltool.update) OUTPUT (in module cwltool.subgraph) output_callback() (cwltool.executors.JobExecutor method) OutputCallbackType (in module cwltool.utils) OutputPortsType (in module cwltool.command_line_tool) overrides_ctx (in module cwltool.load_tool)

P

pack() (in module cwltool.pack) packed_workflow() (cwltool.provenance.ResearchObject method) parallel_steps() (in module cwltool.workflow_job) param_re (in module cwltool.expression) param_str (in module cwltool.expression) ParameterOutputWorkflowException ParametersType (in module cwltool.utils) pass_through_env_vars() (cwltool.mpi.MpiConfig method) PathCheckingMode (class in cwltool.command_line_tool) PathMapper (class in cwltool.pathmapper) posix_path() (in module cwltool.utils) prepare_environment() (cwltool.job.JobBase method) print_js_hint_messages() (in module cwltool.validate_js) print_pack() (in module cwltool.main) print_targets() (in module cwltool.main)

printdeps() (in module cwltool.main) printdot() (in module cwltool.cwlrdf) printrdf() (in module cwltool.cwlrdf) Process (class in cwltool.process) PROCESS_FINISHED_STR (in module cwltool.sandboxjs) process_monitor() (cwltool.job.JobBase method) processDFS() (in module cwltool.checker) processes_to_kill (in module cwltool.utils) ProcessGenerator (class in cwltool.procgenerator) ProcessGeneratorJob (class in cwltool.procgenerator) prospective_prov() (cwltool.provenance_profile.ProvenanceProfile method) prov_deps() (in module cwltool.main) PROVENANCE (in module cwltool.provenance_constants) ProvenanceProfile (class in cwltool.provenance_profile) ProvLogFormatter (class in cwltool.main) ProvOut (in module cwltool.main)

R

random_outdir() (in module cwltool.utils) readable() (cwltool.provenance.WritableBagFile method) realize_input_schema() (in module cwltool.main) realpath() (cwltool.stdfsaccess.StdFsAccess method) receive_output() (cwltool.procgenerator.ProcessGeneratorJob method) (cwltool.workflow.WorkflowStep method) (cwltool.workflow_job.WorkflowJob method) receive_scatter_output() (cwltool.workflow_job.ReceiveScatterOutput method) ReceiveScatterOutput (class in cwltool.workflow_job) record_process_end() (cwltool.provenance_profile.ProvenanceProfile method) record_process_start() (cwltool.provenance_profile.ProvenanceProfile method) recursive_resolve_and_validate_document() (in module cwltool.load_tool) register_mutation() (cwltool.mutation.MutationManager method) register_reader() (cwltool.mutation.MutationManager method) RELAXED (cwltool.command_line_tool.PathCheckingMode attribute) release_reader() (cwltool.mutation.MutationManager method) relink_initialworkdir() (in module cwltool.job) relocateOutputs() (in module cwltool.process) remove_path() (in module cwltool.command_line_tool) replace_refs() (in module cwltool.pack) ResearchObject (class in cwltool.provenance) resolve_and_validate_document() (in module cwltool.load_tool) resolve_ga4gh_tool() (in module cwltool.resolver)

resolve_local() (in module cwltool.resolver) resolve_overrides() (in module cwltool.load_tool) resolve_tool_uri() (in module cwltool.load_tool) ResolverType (in module cwltool.utils) result() (cwltool.procgenerator.ProcessGenerator method) retrieve() (cwltool.secrets.SecretStore method) reversemap() (cwltool.pathmapper.PathMapper method) revmap_file() (in module cwltool.command_line_tool) RO (in module cwltool.provenance_constants) run() (cwltool.command_line_tool.CallbackJob method) (cwltool.command_line_tool.ExpressionJob method) (cwltool.job.CommandLineJob method) (cwltool.job.ContainerCommandLineJob method) (cwltool.job.JobBase method) (cwltool.workflow_job.WorkflowJob method) (in module cwltool.main) run_job() (cwltool.executors.MultithreadedJobExecutor method) run_jobs() (cwltool.executors.JobExecutor method) (cwltool.executors.MultithreadedJobExecutor method) (cwltool.executors.NoopJobExecutor method) (cwltool.executors.SingleJobExecutor method) runtime_context (cwltool.factory.Factory attribute) RuntimeContext (class in cwltool.context)

S

salad_files (in module cwltool.process) scandeps() (in module cwltool.process) scanner() (in module cwltool.expression) ScatterDestinationsType (in module cwltool.utils) ScatterOutputCallbackType (in module cwltool.utils) SCHEMA (in module cwltool.provenance_constants) SCHEMA_ANY (in module cwltool.process) SCHEMA_CACHE (in module cwltool.process) SCHEMA_DIR (in module cwltool.process) SCHEMA_FILE (in module cwltool.process) SecretStore (class in cwltool.secrets) seekable() (cwltool.provenance.WritableBagFile method) seg_double (in module cwltool.expression) seg_index (in module cwltool.expression) seg_single (in module cwltool.expression) seg_symbol (in module cwltool.expression) segment_re (in module cwltool.expression) segments (in module cwltool.expression) select_resources() (cwltool.executors.MultithreadedJobExecutor method) self_check() (cwltool.provenance.ResearchObject method) set_env_vars() (cwltool.mpi.MpiConfig method) set_generation() (cwltool.mutation.MutationManager method) set_log_dir() (in module cwltool.context) setTotal() (cwltool.workflow_job.ReceiveScatterOutput method) setup() (cwltool.pathmapper.PathMapper method) setup_loadingContext() (in module cwltool.main) setup_provenance() (in module cwltool.main) setup_schema() (in module cwltool.main)

SHA1 (in module cwltool.provenance_constants) SHA256 (in module cwltool.provenance_constants) SHA512 (in module cwltool.provenance_constants) shared_file_lock() (in module cwltool.utils) SHELL_COMMAND_TEMPLATE (in module cwltool.job) shortname() (in module cwltool.process) SingleJobExecutor (class in cwltool.executors) singularity_supports_userns() (in module cwltool.singularity_utils) SingularityCommandLineJob (class in cwltool.singularity) SinkType (in module cwltool.utils) size() (cwltool.stdfsaccess.StdFsAccess method) SNAPSHOT (in module cwltool.provenance_constants) SOFTWARE_REQUIREMENTS_ENABLED (in module cwltool.software_requirements) SrcSink (in module cwltool.checker) stage_files() (in module cwltool.process) start_process() (cwltool.provenance_profile.ProvenanceProfile method) static_checker() (in module cwltool.checker) StdFsAccess (class in cwltool.stdfsaccess) STEP (in module cwltool.subgraph) StepType (in module cwltool.utils) store() (cwltool.secrets.SecretStore method) STRICT (cwltool.command_line_tool.PathCheckingMode attribute) subgraph_visit() (in module cwltool.subgraph) substitute() (in module cwltool.builder) SubstitutionError supported_cwl_versions() (in module cwltool.main) supportedProcessRequirements (in module cwltool.process) SuppressLog (class in cwltool.validate_js)

T

TaskQueue (class in cwltool.task_queue) TEXT_PLAIN (in module cwltool.provenance_constants) TMPDIR_LOCK (in module cwltool.executors) tool_resolver() (in module cwltool.resolver)

ToolRequirement (in module cwltool.software_requirements) tostr() (cwltool.builder.Builder method) trim_listing() (in module cwltool.utils) truncate() (cwltool.provenance.WritableBagFile method) try_make_job() (cwltool.workflow_job.WorkflowJob method)

U

UDockerCommandLineJob (class in cwltool.udocker) uniquename() (in module cwltool.process) unset_generation() (cwltool.mutation.MutationManager method) UnsupportedRequirement UP (in module cwltool.subgraph) update() (cwltool.pathmapper.PathMapper method) (in module cwltool.update) updatePathmap() (cwltool.command_line_tool.CommandLineTool method)

UPDATES (in module cwltool.update) upgrade_lock() (in module cwltool.utils) use_custom_schema() (in module cwltool.process) use_standard_schema() (in module cwltool.process) used_artefacts() (cwltool.provenance_profile.ProvenanceProfile method) used_by_step() (in module cwltool.workflow) user_provenance() (cwltool.provenance.ResearchObject method) USER_UUID (in module cwltool.provenance_constants) UUID (in module cwltool.provenance_constants)

V

v1_0to1_1() (in module cwltool.update) v1_1_0dev1to1_1() (in module cwltool.update) v1_1to1_2() (in module cwltool.update) v1_2_0dev1todev2() (in module cwltool.update) v1_2_0dev2todev3() (in module cwltool.update) v1_2_0dev3todev4() (in module cwltool.update) v1_2_0dev4todev5() (in module cwltool.update) v1_2_0dev5to1_2() (in module cwltool.update) validate_hints() (cwltool.process.Process method)

validate_js_expressions() (in module cwltool.validate_js) var_spool_cwl_detector() (in module cwltool.process) versionstring() (in module cwltool.utils) visit() (cwltool.pathmapper.PathMapper method) (cwltool.process.Process method) (cwltool.workflow.Workflow method) (cwltool.workflow.WorkflowStep method) visit_class() (in module cwltool.utils) visit_field() (in module cwltool.utils) visitlisting() (cwltool.pathmapper.PathMapper method)

W

wait_for_next_completion() (cwltool.executors.MultithreadedJobExecutor method) WF4EVER (in module cwltool.provenance_constants) WFDESC (in module cwltool.provenance_constants) WFPROV (in module cwltool.provenance_constants) windows_check() (in module cwltool.main) Workflow (class in cwltool.workflow) WORKFLOW (in module cwltool.provenance_constants) WorkflowException

WorkflowJob (class in cwltool.workflow_job) WorkflowJobStep (class in cwltool.workflow_job) WorkflowStateItem (in module cwltool.utils) WorkflowStatus WorkflowStep (class in cwltool.workflow) WritableBagFile (class in cwltool.provenance) write() (cwltool.provenance.WritableBagFile method) write_bag_file() (cwltool.provenance.ResearchObject method)