Common Workflow Language (CWL) Command Line Tool Description, draft 3 §
This version:
Current version:
Authors:
- Peter Amstutz, Arvados Project, Curoverse (now peter.amstutz@curii.com)
- Nebojša Tijanić nebojsa.tijanic@sbgenomics.com, Seven Bridges Genomics
Contributers:
- Brad Chapman bchapman@hsph.harvard.edu, Harvard Chan School of Public Health
- John Chilton jmchilton@gmail.com, Galaxy Project, Pennsylvania State University
- Michael R. Crusoe crusoe@ucdavis.edu, University of California, Davis
- Andrey Kartashov Andrey.Kartashov@cchmc.org, Cincinnati Children's Hospital
- Dan Leehr dan.leehr@duke.edu, Duke University
- Hervé Ménager herve.menager@gmail.com, Institut Pasteur
- Stian Soiland-Reyes soiland-reyes@cs.manchester.ac.uk, University of Manchester
- Luka Stojanovic luka.stojanovic@sbgenomics.com, Seven Bridges Genomics
Abstract §
A Command Line Tool is a non-interactive executable program that reads some input, performs a computation, and terminates after producing some output. Command line programs are a flexible unit of code sharing and reuse, unfortunately the syntax and input/output semantics among command line programs is extremely heterogeneous. A common layer for describing the syntax and semantics of programs can reduce this incidental complexity by providing a consistent way to connect programs together. This specification defines the Common Workflow Language (CWL) Command Line Tool Description, a vendor-neutral standard for describing the syntax and input/output semantics of command line programs.
Status of This Document §
This document is the product of the Common Workflow Language working group. The latest version of this document is available in the "draft-3" directory at
https://github.com/common-workflow-language/common-workflow-language
The products of the CWL working group (including this document) are made available under the terms of the Apache License, version 2.0.
Table of contents
1. Introduction §
The Common Workflow Language (CWL) working group is an informal, multi-vendor working group consisting of various organizations and individuals that have an interest in portability of data analysis workflows. The goal is to create specifications like this one that enable data scientists to describe analysis tools and workflows that are powerful, easy to use, portable, and support reproducibility.
1.1 Introduction to draft 3 §
This specification represents the third milestone of the CWL group. Since draft-2, this draft introduces the following major changes and additions:
- Greatly simplified naming within a document with scoped identifiers, as described in the Schema Salad specification.
- The draft-2 concept of pluggable expression engines has been replaced by a streamlined expression syntax and standardization on Javascript.
- File objects can now include a
formatfield to indicate the file type. - The addition of ShellCommandRequirement.
- The addition of ResourceRequirement.
- The separation of CommandLineTool and Workflow components into separate specifications.
1.2 Purpose §
Standalone programs are a flexible and interoperable form of code reuse. Unlike monolithic applications, applications and analysis workflows which are composed of multiple separate programs can be written in multiple languages and execute concurrently on multiple hosts. However, POSIX does not dictate computer-readable grammar or semantics for program input and output, resulting in extremely heterogeneous command line grammar and input/output semantics among program. This a particular problem in distributed computing (multi-node compute clusters) and virtualized environments (such as Docker containers) where it is often necessary to provision resources such as input files before executing the program.
Often this is gap is filled by hard coding program invocation and implicitly assuming requirements will be met, or abstracting program invocation with wrapper scripts or descriptor documents. Unfortunately, where these approaches are application or platform specific it creates a significant barrier to reproducibility and portability, as methods developed for one platform must be manually ported to be used on new platforms. Similarly it creates redundant work, as wrappers for popular tools must be rewritten for each application or platform in use.
The Common Workflow Language Command Line Tool Description is designed to provide a common standard description of grammar and semantics for invoking programs used in data-intensive fields such as Bioinformatics, Chemistry, Physics, Astronomy, and Statistics. This specification defines a precise data and execution model for Command Line Tools that can be implemented on a variety of computing platforms, ranging from a single workstation to cluster, grid, cloud, and high performance computing platforms.
1.3 References to Other Specifications §
Javascript Object Notation (JSON): http://json.org
JSON Linked Data (JSON-LD): http://json-ld.org
YAML: http://yaml.org
Avro: https://avro.apache.org/docs/current/spec.html
Uniform Resource Identifier (URI) Generic Syntax: https://tools.ietf.org/html/rfc3986)
Portable Operating System Interface (POSIX.1-2008): http://pubs.opengroup.org/onlinepubs/9699919799/
Resource Description Framework (RDF): http://www.w3.org/RDF/
1.4 Scope §
This document describes CWL syntax, execution, and object model. It is not intended to document a CWL specific implementation, however it may serve as a reference for the behavior of conforming implementations.
1.5 Terminology §
The terminology used to describe CWL documents is defined in the Concepts section of the specification. The terms defined in the following list are used in building those definitions and in describing the actions of an CWL implementation:
may: Conforming CWL documents and CWL implementations are permitted but not required to behave as described.
must: Conforming CWL documents and CWL implementations are required to behave as described; otherwise they are in error.
error: A violation of the rules of this specification; results are undefined. Conforming implementations may detect and report an error and may recover from it.
fatal error: A violation of the rules of this specification; results are undefined. Conforming implementations must not continue to execute the current process and may report an error.
at user option: Conforming software may or must (depending on the modal verb in the sentence) behave as described; if it does, it must provide users a means to enable or disable the behavior described.
deprecated: Conforming software may implement a behavior for backwards compatibility. Portable CWL documents should not rely on deprecated behavior. Behavior marked as deprecated may be removed entirely from future revisions of the CWL specification.
2. Data model §
2.1 Data concepts §
An object is a data structure equivalent to the "object" type in JSON, consisting of a unordered set of name/value pairs (referred to here as fields) and where the name is a string and the value is a string, number, boolean, array, or object.
A document is a file containing a serialized object, or an array of objects.
A process is a basic unit of computation which accepts input data, performs some computation, and produces output data.
An input object is an object describing the inputs to a invocation of process.
An output object is an object describing the output of an invocation of a process.
An input schema describes the valid format (required fields, data types) for an input object.
An output schema describes the valid format for a output object.
Metadata is information about workflows, tools, or input items that is not used directly in the computation.
2.2 Syntax §
CWL documents must consist of an object or array of objects represented using JSON or YAML syntax. Upon loading, a CWL implementation must apply the preprocessing steps described in the Semantic Annotations for Linked Avro Data (SALAD) Specification. A implementation may formally validate the structure of a CWL document using SALAD schemas located at https://github.com/common-workflow-language/common-workflow-language/tree/master/draft-3
2.3 Identifiers §
If an object contains an id field, that is used to uniquely identify the
object in that document. The value of the id field must be unique over the
entire document. Identifiers may be resolved relative to other the document
base and/or other identifiers following the rules are described in the
Schema Salad specification.
An implementation may choose to only honor references to object types for
which the id field is explicitly listed in this specification.
2.4 Document preprocessing §
An implementation must resolve $import and $include directives as described in the Schema Salad specification.
2.5 Extensions and Metadata §
Input metadata (for example, a lab sample identifier) may be represented within a tool or workflow using input parameters which are explicitly propagated to output. Future versions of this specification may define additional facilities for working with input/output metadata.
Implementation extensions not required for correct execution (for example,
fields related to GUI presentation) and metadata about the tool or workflow
itself (for example, authorship for use in citations) may be provided as
additional fields on any object. Such extensions fields must use a namespace
prefix listed in the $namespaces section of the document as described in the
Schema Salad specification.
Implementation extensions which modify execution semantics must be listed in
the requirements field.
3. Execution model §
3.1 Execution concepts §
A parameter is a named symbolic input or output of process, with an associated datatype or schema. During execution, values are assigned to parameters to make the input object or output object used for concrete process invocation.
A command line tool is a process characterized by the execution of a standalone, non-interactive program which is invoked on some input, produces output, and then terminates.
A workflow is a process characterized by multiple subprocess steps, where step outputs are connected to the inputs of other downstream steps to form a directed graph, and independent steps may run concurrently.
A runtime environment is the actual hardware and software environment when executing a command line tool. It includes, but is not limited to, the hardware architecture, hardware resources, operating system, software runtime (if applicable, such as the Python interpreter or the JVM), libraries, modules, packages, utilities, and data files required to run the tool.
A workflow platform is a specific hardware and software implementation capable of interpreting CWL documents and executing the processes specified by the document. The responsibilities of the workflow platform may include scheduling process invocation, setting up the necessary runtime environment, making input data available, invoking the tool process, and collecting output.
A workflow platform may choose to only implement the Command Line Tool Description part of the CWL specification.
It is intended that the workflow platform has broad leeway outside of this specification to optimize use of computing resources and enforce policies not covered by this specification. Some areas that are currently out of scope for CWL specification but may be handled by a specific workflow platform include:
- Data security and permissions.
- Scheduling tool invocations on remote cluster or cloud compute nodes.
- Using virtual machines or operating system containers to manage the runtime (except as described in DockerRequirement).
- Using remote or distributed file systems to manage input and output files.
- Transforming file paths.
- Determining if a process has previously been executed, skipping it and reusing previous results.
- Pausing, resuming or checkpointing processes or workflows.
Conforming CWL processes must not assume anything about the runtime environment or workflow platform unless explicitly declared though the use of process requirements.
3.2 Generic execution process §
The generic execution sequence of a CWL process (including workflows and command line line tools) is as follows.
- Load, process and validate a CWL document, yielding a process object.
- Load input object.
- Validate the input object against the
inputsschema for the process. - Validate that process requirements are met.
- Perform any further setup required by the specific process type.
- Execute the process.
- Capture results of process execution into the output object.
- Validate the output object against the
outputsschema for the process. - Report the output object to the process caller.
3.3 Requirements and hints §
A process requirement modifies the semantics or runtime environment of a process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
A hint is similar to a requirement, however it is not an error if an implementation cannot satisfy all hints. The implementation may report a warning if a hint cannot be satisfied.
Requirements are inherited. A requirement specified in a Workflow applies to all workflow steps; a requirement specified on a workflow step will apply to the process implementation.
If the same process requirement appears at different levels of the
workflow, the most specific instance of the requirement is used, that is,
an entry in requirements on a process implementation such as
CommandLineTool will take precedence over an entry in requirements
specified in a workflow step, and an entry in requirements on a workflow
step takes precedence over the workflow. Entries in hints are resolved
the same way.
Requirements override hints. If a process implementation provides a
process requirement in hints which is also provided in requirements by
an enclosing workflow or workflow step, the enclosing requirements takes
precedence.
3.4 Parameter references §
Parameter references are denoted by the syntax $(...) and may be used in any
field permitting the pseudo-type Expression, as specified by this document.
Conforming implementations must support parameter references. Parameter
references use the following subset of
Javascript/ECMAScript 5.1
syntax.
In the following BNF grammar, character classes and grammar rules are denoted in '{}', '-' denotes exclusion from a character class, '(())' denotes grouping, '|' denotes alternates, trailing '*' denotes zero or more repeats, '+' denote one or more repeats, all other characters are literal values.
| symbol:: | {Unicode alphanumeric}+ |
| singleq:: | [' (( {character - '} | \' ))* '] |
| doubleq:: | [" (( {character - "} | \" ))* "] |
| index:: | [ {decimal digit}+ ] |
| segment:: | . {symbol} | {singleq} | {doubleq} | {index} |
| parameter:: | $( {symbol} {segment}*) |
Use the following algorithm to resolve a parameter reference:
- Match the leading symbol as key
- Look up the key in the parameter context (described below) to get the current value. It is an error if the key is not found in the parameter context.
- If there are no subsequent segments, terminate and return current value
- Else, match the next segment
- Extract the symbol, string, or index from the segment as key
- Look up the key in current value and assign as new current value. If the key is a symbol or string, the current value must be an object. If the key is an index, the current value must be an array or string. It is an error if the key does not match the required type, or the key is not found or out of range.
- Repeat steps 3-6
The root namespace is the parameter context. The following parameters must be provided:
inputs: The input object to the current Process.self: A context-specific value. The contextual values for 'self' are documented for specific fields elsewhere in this specification. If a contextual value of 'self' is not documented for a field, it must be 'null'.runtime: An object containing configuration details. Specific to the process type. An implementation may provide may provide opaque strings for any or all fields ofruntime. These must be filled in by the platform after processing the Tool but before actual execution. Parameter references and expressions may only use the literal string value of the field and must not perform computation on the contents.
If the value of a field has no leading or trailing non-whitespace characters around a parameter reference, the effective value of the field becomes the value of the referenced parameter, preserving the return type.
If the value of a field has non-whitespace leading or trailing characters around an parameter reference, it is subject to string interpolation. The effective value of the field is a string containing the leading characters; followed by the string value of the parameter reference; followed by the trailing characters. The string value of the parameter reference is its textual JSON representation with the following rules:
- Leading and trailing quotes are stripped from strings
- Objects entries are sorted by key
Multiple parameter references may appear in a single field. This case is must be treated as a string interpolation. After interpolating the first parameter reference, interpolation must be recursively applied to the trailing characters to yield the final string value.
3.5 Expressions §
An expression is a fragment of Javascript/ECMAScript 5.1 code which is evaluated by the workflow platform to affect the inputs, outputs, or behavior of a process. In the generic execution sequence, expressions may be evaluated during step 5 (process setup), step 6 (execute process), and/or step 7 (capture output). Expressions are distinct from regular processes in that they are intended to modify the behavior of the workflow itself rather than perform the primary work of the workflow.
To declare the use of expressions, the document must include the process
requirement InlineJavascriptRequirement. Expressions may be used in any
field permitting the pseudo-type Expression, as specified by this
document.
Expressions are denoted by the syntax $(...) or ${...}. A code
fragment wrapped in the $(...) syntax must be evaluated as a
ECMAScript expression. A
code fragment wrapped in the ${...} syntax must be evaluated as a
EMACScript function body
for an anonymous, zero-argument function. Expressions must return a valid JSON
data type: one of null, string, number, boolean, array, object.
Implementations must permit any syntactically valid Javascript and account
for nesting of parenthesis or braces and that strings that may contain
parenthesis or braces when scanning for expressions.
The runtime must include any code defined in the "expressionLib" field of InlineJavascriptRequirement prior to executing the actual expression.
Before executing the expression, the runtime must initialize as global variables the fields of the parameter context described above.
The effective value of the field after expression evaluation follows the same rules as parameter references discussed above. Multiple expressions may appear in a single field.
Expressions must be evaluated in an isolated context (a "sandbox") which permits no side effects to leak outside the context. Expressions also must be evaluated in Javascript strict mode.
The order in which expressions are evaluated is undefined except where otherwise noted in this document.
An implementation may choose to implement parameter references by evaluating as a Javascript expression. The results of evaluating parameter references must be identical whether implemented by Javascript evaluation or some other means.
Implementations may apply other limits, such as process isolation, timeouts, and operating system containers/jails to minimize the security risks associated with running untrusted code embedded in a CWL document.
3.6 Success and failure §
A completed process must result in one of success, temporaryFailure or
permanentFailure states. An implementation may choose to retry a process
execution which resulted in temporaryFailure. An implementation may
choose to either continue running other steps of a workflow, or terminate
immediately upon permanentFailure.
If any step of a workflow execution results in
permanentFailure, then the workflow status ispermanentFailure.If one or more steps result in
temporaryFailureand all other steps completesuccessor are not executed, then the workflow status istemporaryFailure.If all workflow steps are executed and complete with
success, then the workflow status issuccess.
3.7 Executing CWL documents as scripts §
By convention, a CWL document may begin with #!/usr/bin/env cwl-runner
and be marked as executable (the POSIX "+x" permission bits) to enable it
to be executed directly. A workflow platform may support this mode of
operation; if so, it must provide cwl-runner as an alias for the
platform's CWL implementation.
A CWL input object document may similarly begin with #!/usr/bin/env cwl-runner and be marked as executable. In this case, the input object
must include the field cwl:tool supplying a URI to the default CWL
document that should be executed using the fields of the input object as
input parameters.
4. Running a Command §
To accommodate the enormous variety in syntax and semantics for input, runtime environment, invocation, and output of arbitrary programs, a CommandLineTool defines an "input binding" that describes how to translate abstract input parameters to an concrete program invocation, and an "output binding" that describes how to generate output parameters from program output.
4.1 Input binding §
The tool command line is built by applying command line bindings to the
input object. Bindings are listed either as part of an input
parameter using the inputBinding field, or
separately using the arguments field of the CommandLineTool.
The algorithm to build the command line is as follows. In this algorithm, the sort key is a list consisting of one or more numeric or string elements. Strings are sorted lexicographically based on UTF-8 encoding.
Collect
CommandLineBindingobjects fromarguments. Assign a sorting key[position, i]wherepositionisCommandLineBinding.positionandiis the index in theargumentslist.Collect
CommandLineBindingobjects from theinputsschema and associate them with values from the input object. Where the input type is a record, array, or map, recursively walk the schema and input object,
Create a sorting key by taking the value of the
positionfield at each level leading to each leaf binding object. Ifpositionis not specified, it is not added to the sorting key. For bindings on arrays and maps, the sorting key must include the array index or map key following the position. If and only if two bindings have the same sort key, the tie must be broken using the ordering of the field or parameter name immediately containing the leaf binding.Sort elements using the assigned sorting keys. Numeric entries sort before strings.
In the sorted order, apply the rules defined in
CommandLineBindingto convert bindings to actual command line elements.Insert elements from
baseCommandat the beginning of the command line.
4.2 Runtime environment §
All files listed in the input object must be made available in the runtime environment. The implementation may use a shared or distributed file system or transfer files via explicit download. Implementations may choose not to provide access to files not explicitly specified in the input object or process requirements.
Output files produced by tool execution must be written to the designated output directory. The initial current working directory when executing the tool must be the designated output directory.
Files may also be written to the designated temporary directory. This directory must be isolated and not shared with other processes. Any files written to the designated temporary directory may be automatically deleted by the workflow platform immediately after the tool terminates.
For compatibility, files may be written to the system temporary directory
which must be located at /tmp. Because the system temporary directory may be
shared with other processes on the system, files placed in the system temporary
directory are not guaranteed to be deleted automatically. Correct tools must
clean up temporary files written to the system temporary directory. A tool
must not use the system temporary directory as a backchannel communication with
other tools. It is valid for the system temporary directory to be the same as
the designated temporary directory.
When executing the tool, the tool must execute in a new, empty environment with only the environment variables described below; the child process must not inherit environment variables from the parent process except as specified or at user option.
HOMEmust be set to the designated output directory.TMPDIRmust be set to the designated temporary directory. when the tool invocation and output collection is complete.PATHmay be inherited from the parent process, except when run in a container that provides its ownPATH.- Variables defined by EnvVarRequirement
- The default environment of the container, such as when using DockerRequirement
An implementation may forbid the tool from writing to any location in the runtime environment file system other than the designated temporary directory, system temporary directory, and designated output directory. An implementation may provide read-only input files, and disallow in-place update of input files. The designated temporary directory, system temporary directory and designated output directory may each reside on different mount points on different file systems.
An implementation may forbid the tool from directly accessing network resources. Correct tools must not assume any network access. Future versions of the specification may incorporate optional process requirements that describe the networking needs of a tool.
The runtime section available in parameter references
and expressions contains the following fields. As noted
earlier, an implementation may perform deferred resolution of runtime fields by providing
opaque strings for any or all of the following fields; parameter references
and expressions may only use the literal string value of the field and must
not perform computation on the contents.
runtime.outdir: an absolute path to the designated output directoryruntime.tmpdir: an absolute path to the designated temporary directoryruntime.cores: number of CPU cores reserved for the tool processruntime.ram: amount of RAM in mebibytes (2**20) reserved for the tool processruntime.outdirSize: reserved storage space available in the designated output directoryruntime.tmpdirSize: reserved storage space available in the designated temporary directory
See ResourceRequirement for details on how to describe the hardware resources required by a tool.
The standard input stream and standard output stream may be redirected as
described in the stdin and stdout fields.
4.3 Execution §
Once the command line is built and the runtime environment is created, the actual tool is executed.
The standard error stream and standard output stream (unless redirected by
setting stdout) may be captured by platform logging facilities for
storage and reporting.
Tools may be multithreaded or spawn child processes; however, when the parent process exits, the tool is considered finished regardless of whether any detached child processes are still running. Tools must not require any kind of console, GUI, or web based user interaction in order to start and run to completion.
The exit code of the process indicates if the process completed
successfully. By convention, an exit code of zero is treated as success
and non-zero exit codes are treated as failure. This may be customized by
providing the fields successCodes, temporaryFailCodes, and
permanentFailCodes. An implementation may choose to default unspecified
non-zero exit codes to either temporaryFailure or permanentFailure.
4.4 Output binding §
If the output directory contains a file named "cwl.output.json", that file
must be loaded and used as the output object. Otherwise, the output object
must be generated by walking the parameters listed in outputs and
applying output bindings to the tool output. Output bindings are
associated with output parameters using the outputBinding field. See
CommandOutputBinding for details.
5. CommandLineTool §
This defines the schema of the CWL Command Line Tool Description document.
Fields
inputsDefines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used to build a user interface for constructing the input object.
outputsDefines the parameters representing the output of the process. May be used to generate and/or validate the output object.
baseCommandSpecifies the program to execute. If the value is an array, the first
element is the program to execute, and subsequent elements are placed
at the beginning of the command line in prior to any command line
bindings. If the program includes a path separator character it must
be an absolute path, otherwise it is an error. If the program does not
include a path separator, search the $PATH variable in the runtime
environment of the workflow runner find the absolute path of the
executable.
requirementsDeclares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
hintsDeclares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
argumentsCommand line bindings which are not directly associated with input parameters.
stdinA path to a file whose contents must be piped into the command's standard input stream.
stdoutCapture the command's standard output stream to a file written to the designated output directory.
If stdout is a string, it specifies the file name to use.
If stdout is an expression, the expression is evaluated and must
return a string with the file name to use to capture stdout. If the
return value is not a string, or the resulting path contains illegal
characters (such as the path separator /) it is an error.
temporaryFailCodesExit codes that indicate the process failed due to a possibly temporary condition, where excuting the process with the same runtime environment and inputs may produce different results.
permanentFailCodesExit codes that indicate the process failed due to a permanent logic error, where excuting the process with the same runtime environment and same inputs is expected to always fail.
5.1 CommandInputParameter §
An input parameter for a CommandLineTool.
Fields
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
typeSpecify valid types of data that may be assigned to this parameter.
inputBindingDescribes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters.
5.1.1 Expression §
Not a real type. Indicates that a field must allow runtime parameter references. If InlineJavascriptRequirement is declared and supported by the platform, the field must also allow Javascript expressions.
Symbols
| symbol | description |
|---|---|
ExpressionPlaceholder |
5.1.2 CWLType §
Extends primitive types with the concept of a file as a first class type.
Symbols
| symbol | description |
|---|---|
null | no value |
boolean | a binary value |
int | 32-bit signed integer |
long | 64-bit signed integer |
float | single precision (32-bit) IEEE 754 floating-point number |
double | double precision (64-bit) IEEE 754 floating-point number |
string | Unicode character sequence |
null | no value |
boolean | a binary value |
int | 32-bit signed integer |
long | 64-bit signed integer |
float | single precision (32-bit) IEEE 754 floating-point number |
double | double precision (64-bit) IEEE 754 floating-point number |
string | Unicode character sequence |
File | A File object |
5.1.3 File §
Represents a file (or group of files if secondaryFiles is specified) that
must be accessible by tools using standard POSIX file system call API such as
open(2) and read(2).
Fields
classFileMust be File to indicate this object describes a file.
checksumOptional hash code for validating file integrity. Currently must be in the form "sha1$ + hexidecimal string" using the SHA-1 algorithm.
secondaryFilesA list of additional files that are associated with the primary file
and must be transferred alongside the primary file. Examples include
indexes of the primary file, or external references which must be
included when loading primary document. A file object listed in
secondaryFiles may itself include secondaryFiles for which the same
rules apply.
formatThe format of the file. This must be a URI of a concept node that represents the file format, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
Reasoning about format compatability must be done by checking that an
input file format is the same, owl:equivalentClass or
rdfs:subClassOf the format required by the input parameter.
owl:equivalentClass is transitive with rdfs:subClassOf, e.g. if
<B> owl:equivalentClass <C> and <B> owl:subclassOf <A> then infer
<C> owl:subclassOf <A>.
File format ontologies may be provided in the "$schema" metadata at the
root of the document. If no ontologies are specified in $schema, the
runtime may perform exact file format matches.
5.1.4 CommandInputRecordSchema §
Fields
typerecordMust be record
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.1.4.1 CommandInputRecordField §
Fields
typeThe field type
5.1.4.1.1 PrimitiveType §
Salad data types are based on Avro schema declarations. Refer to the Avro schema declaration documentation for detailed information.
Symbols
| symbol | description |
|---|---|
null | |
boolean | |
int | |
long | |
float | |
double | |
string |
5.1.4.1.2 CommandInputEnumSchema §
Fields
typeenumMust be enum
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.1.4.1.2.1 CommandLineBinding §
When listed under inputBinding in the input schema, the term
"value" refers to the the corresponding value in the input object. For
binding objects listed in CommandLineTool.arguments, the term "value"
refers to the effective value after evaluating valueFrom.
The binding behavior when building the command line depends on the data type of the value. If there is a mismatch between the type described by the input schema and the effective value, such as resulting from an expression evaluation, an implementation must use the data type of the effective value.
string: Add
prefixand the string to the command line.number: Add
prefixand decimal representation to command line.boolean: If true, add
prefixto the command line. If false, add nothing.File: Add
prefixand the value ofFile.pathto the command line.array: If
itemSeparatoris specified, addprefixand the join the array into a single string withitemSeparatorseparating the items. Otherwise first addprefix, then recursively process individual elements.object: Add
prefixonly, and recursively add object fields for whichinputBindingis specified.null: Add nothing.
Fields
loadContentsOnly valid when type: File or is an array of items: File.
Read up to the first 64 KiB of text from the file and place it in the "contents" field of the file object for use by expressions.
separateIf true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument.
itemSeparatorJoin the array elements into a single string with the elements
separated by by itemSeparator.
valueFromIf valueFrom is a constant string value, use this as the value and
apply the binding rules above.
If valueFrom is an expression, evaluate the expression to yield the
actual value to use to build the command line and apply the binding
rules above. If the inputBinding is associated with an input
parameter, the value of self in the expression will be the value of the
input parameter.
When a binding is part of the CommandLineTool.arguments field,
the valueFrom field is required.
shellQuoteIf ShellCommandRequirement is in the requirements for the current command,
this controls whether the value is quoted on the command line (default is true).
Use shellQuote: false to inject metacharacters for operations such as pipes.
5.1.4.1.3 CommandInputArraySchema §
Fields
typearrayMust be array
itemsDefines the type of the array elements.
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.1.5 Any §
The Any type validates for any non-null value.
Symbols
| symbol | description |
|---|---|
Any |
5.2 CommandOutputParameter §
An output parameter for a CommandLineTool.
Fields
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
typeSpecify valid types of data that may be assigned to this parameter.
5.2.1 CommandOutputRecordSchema §
Fields
typerecordMust be record
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.2.1.1 CommandOutputRecordField §
Fields
typeThe field type
5.2.1.1.1 CommandOutputEnumSchema §
Fields
typeenumMust be enum
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.2.1.1.1.1 CommandOutputBinding §
Describes how to generate an output parameter based on the files produced by a CommandLineTool.
The output parameter is generated by applying these operations in the following order:
- glob
- loadContents
- outputEval
Fields
globFind files relative to the output directory, using POSIX glob(3) pathname matching. If provided an array, find files that match any pattern in the array. If provided an expression, the expression must return a string or an array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files which actually exist.
loadContentsFor each file matched in glob, read up to
the first 64 KiB of text from the file and place it in the contents
field of the file object for manipulation by outputEval.
outputEvalEvaluate an expression to generate the output value. If glob was
specified, the value of self must be an array containing file objects
that were matched. If no files were matched, self' must be a zero length array; if a single file was matched, the value of selfis an array of a single element. Additionally, ifloadContentsistrue, the File objects must include up to the first 64 KiB of file contents in the contents` field.
5.2.1.1.2 CommandOutputArraySchema §
Fields
typearrayMust be array
itemsDefines the type of the array elements.
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.3 InlineJavascriptRequirement §
Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation.
Fields
expressionLibAdditional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions.
5.4 SchemaDefRequirement §
This field consists of an array of type definitions which must be used when
interpreting the inputs and outputs fields. When a type field
contain a URI, the implementation must check if the type is defined in
schemaDefs and use that definition. If the type is not found in
schemaDefs, it is an error. The entries in schemaDefs must be
processed in the order listed such that later schema definitions may refer
to earlier schema definitions.
Fields
typesThe list of type definitions.
5.4.1 InputRecordSchema §
Fields
typerecordMust be record
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.4.1.1 InputRecordField §
Fields
typeThe field type
5.4.1.1.1 InputEnumSchema §
Fields
typeenumMust be enum
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.4.1.1.2 InputArraySchema §
Fields
typearrayMust be array
itemsDefines the type of the array elements.
secondaryFilesOnly valid when type: File or is an array of items: File.
Describes files that must be included alongside the primary file(s).
If the value is an expression, the value of self in the expression
must be the primary input or output File to which this binding applies.
If the value is a string, it specifies that the following pattern should be applied to the primary file:
- If string begins with one or more caret
^characters, for each caret, remove the last file extension from the path (the last period.and all following characters). If there are no file extensions, the path is unchanged. - Append the remainder of the string to the end of the file path.
formatOnly valid when type: File or is an array of items: File.
For input parameters, this must be one or more URIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match.
For output parameters, this is the file format that will be assigned to the output parameter.
streamableOnly valid when type: File or is an array of items: File.
A value of true indicates that the file is read or written
sequentially without seeking. An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe. Default: false.
5.5 DockerRequirement §
Indicates that a workflow component should be run in a Docker container, and specifies how to fetch or build the image.
If a CommandLineTool lists DockerRequirement under
hints or requirements, it may (or must) be run in the specified Docker
container.
The platform must first acquire or install the correct Docker image as
specified by dockerPull, dockerImport, dockerLoad or dockerFile.
The platform must execute the tool in the container using docker run with
the appropriate Docker image and tool command line.
The workflow platform may provide input files and the designated output directory through the use of volume bind mounts. The platform may rewrite file paths in the input object to correspond to the Docker bind mounted locations.
When running a tool contained in Docker, the workflow platform must not assume anything about the contents of the Docker container, such as the presence or absence of specific software, except to assume that the generated command line represents a valid command within the runtime environment of the container.
Interaction with other requirements §
If EnvVarRequirement is specified alongside a
DockerRequirement, the environment variables must be provided to Docker
using --env or --env-file and interact with the container's preexisting
environment as defined by Docker.
Fields
dockerLoadSpecify a HTTP URL from which to download a Docker image using docker load.
dockerFileSupply the contents of a Dockerfile which will be built using docker build.
dockerImportProvide HTTP URL to download and gunzip a Docker images using `docker import.
dockerImageIdThe image id that will be used for docker run. May be a
human-readable image name or the image identifier hash. May be skipped
if dockerPull is specified, in which case the dockerPull image id
must be used.
dockerOutputDirectorySet the designated output directory to a specific location inside the Docker container.
5.6 CreateFileRequirement §
Define a list of files that must be created by the workflow
platform in the designated output directory prior to executing the command
line tool. See FileDef for details.
Fields
5.7 FileDef §
Define a file that must be placed in the designated output directory prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template.
Fields
fileContentIf the value is a string literal or an expression which evaluates to a string, a new file must be created with the string as the file contents.
If the value is an expression that evaluates to a File object, this indicates the referenced file should be added to the designated output directory prior to executing the tool.
Files added in this way may be read-only, and may be provided by bind mounts or file system links to avoid unnecessary copying of the input file.
5.8 EnvVarRequirement §
Define a list of environment variables which will be set in the
execution environment of the tool. See EnvironmentDef for details.
Fields
5.9 EnvironmentDef §
Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input.
Fields
5.10 ShellCommandRequirement §
Modify the behavior of CommandLineTool to generate a single string
containing a shell command line. Each item in the argument list must be
joined into a string separated by single spaces and quoted to prevent
intepretation by the shell, unless CommandLineBinding for that argument
contains shellQuote: false. If shellQuote: false is specified, the
argument is joined into the command string without quoting, which allows
the use of shell metacharacters such as | for pipes.
Fields
5.11 ResourceRequirement §
Specify basic hardware resource requirements.
"min" is the minimum amount of a resource that must be reserved to schedule a job. If "min" cannot be satisfied, the job should not be run.
"max" is the maximum amount of a resource that the job shall be permitted to use. If a node has sufficient resources, multiple jobs may be scheduled on a single node provided each job's "max" resource requirements are met. If a job attempts to exceed its "max" resource allocation, an implementation may deny additional resources, which may result in job failure.
If "min" is specified but "max" is not, then "max" == "min" If "max" is specified by "min" is not, then "min" == "max".
It is an error if max < min.
It is an error if the value of any of these fields is negative.
If neither "min" nor "max" is specified for a resource, an implementation may provide a default.
Fields
tmpdirMinMinimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
tmpdirMaxMaximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
outdirMinMinimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
outdirMaxMaximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
5.12 CWLVersions §
Version symbols for published CWL document versions.
Symbols
| symbol | description |
|---|---|
draft-2 | |
draft-3.dev1 | |
draft-3.dev2 | |
draft-3.dev3 | |
draft-3.dev4 | |
draft-3.dev5 | |
draft-3 |