Common Workflow Language reference implementation
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Python version support policy
Process generator
API Reference
Common Workflow Language reference implementation
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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)
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