RED-CWL 0 Specification

RED-CWL 0 is a subset of the CWL 1.0 CommandLineTool Description reflects the current (incomplete) implementation status.

The CWL reference implementation cwltool requires a *.cwl file as generic description of CommandLineTool and a *.yml job file to define an input object, that contains actual parameters to run the experiment. In contrast, a RED file embeds the contents of a *.cwl file under the cli keyword and embeds the input object under the inputs keyword. Depending on the RED execution engine, defining an output object might be optional and can be embedded under the outputs keyword.

The RED-CWL description can be extracted from a RED file’s cli section and stored in a *.cwl file. Since RED-CWL is a subset of the CWL standard, this extracted description should always be compatible with CWL runtimes like cwltool. On the other hand, not every CWL description can be embedded into a RED file without modification.

This spec refers to individial sections of the CWL 1.0 CommandLineTool Description to define wether a certain part of the standard is supported or not.

Data model

Document preprocessing

CWL 1.0 - 2.4 Document preprocessing

Optional inputs and outputs can be defined as <T>?. Input arrays can be defined as <T>[]. Optional input arrays can be defined as <T>[]?. <T> refers to the input type. Output arrays are not allowed.

Running a Command

Runtime Environment

CWL 1.0 - 4.2 Document preprocessing

Setting runtime parameters like runtime.ram is not supported. In the context of RED, this information is part of the container section, because the container engine enforces these settings.

In addtion, the resource requirements of a CLI tool are in many cases influenced by the input data size. This makes resource requirements more of an experiment setting than a CLI tool setting.

CommandLineTool

CWL 1.0 - 5 CommandLineTool

Field	Supported	Description
inputs	partly	only `map<id, type \| CommandInputParameter>`
outputs	partly	only `map<id, type \| CommandInputParameter>`
class	yes
id	no
requirements	no
hints	no
label	no
doc	yes
cwlVersion	yes
baseCommand	yes
arguments	no
stdin	no
stdout	partly	only `string`
stderr	partly	only `string`
successCodes	no
temporaryFailCodes	no
permanentFailCodes	no

CommandInputParameter

CWL 1.0 - 5.1 CommandInputParameter

Field	Supported	Description
id	no	because `inputs` only supports `map<id, type \| CommandInputParameter>`
label	no
secondaryFiles	no
streamable	no
doc	yes
format	no
inputBinding	yes
default	no
type	partly	only `string`, `CWLType`

Expression

CWL 1.0 - 5.1.1 Expression

Symbol	Supported	Description
ExpressionPlaceholder	partly	only in RED `outputs` to reference `inputs`

CommandLineBinding

CWL 1.0 - 5.1.2 CommandLineBinding

Field	Supported	Description
loadContents	no
position	yes
prefix	yes
separate	yes
itemSeparator	yes
valueFrom	no
shellQuote	no

Any

CWL 1.0 - 5.1.3 Any

Not supported.

CWLType

CWL 1.0 - 5.1.4 CWLType

Symbol	Supported	Description
null	yes
boolean	yes
int	yes
long	yes
float	yes
double	yes
string	yes
File	yes
Directory	yes

File

CWL 1.0 - 5.1.5 File

Supported in RED inputs section.

Field	Supported	Description
class	yes
location	no	because RED introduces the `connector` field, that replaces `location`
path	auto	automatically set by execution engine
basename	yes
dirname	yes
nameroot	auto	automatically set by execution engine
nameext	auto	automatically set by execution engine
checksum	yes
size	yes
secondaryFiles	no
format	no
contents	no

CommandInputRecordSchema

CWL 1.0 - 5.1.6 CommandInputRecordSchema

Not supported.

CommandInputRecordField

CWL 1.0 - 5.1.7 CommandInputRecordField

Not supported.

CommandInputRecordSchema

CWL 1.0 - 5.1.6 CommandInputRecordSchema

Not supported.

CommandInputRecordField

CWL 1.0 - 5.1.7 CommandInputRecordField

Not supported.

CommandInputEnumSchema

CWL 1.0 - 5.1.7.1 CommandInputEnumSchema

Not supported.

CommandInputArraySchema

CWL 1.0 - 5.1.7.2 CommandInputArraySchema

https://www.commonwl.org/v1.0/CommandLineTool.html#Document_preprocessing

Not supported, but arrays can be specified using type: <T>[] as described in CWL 1.0 - 2.4 Document preprocessing.

CommandOutputParameter

CWL 1.0 - 5.2 CommandOutputParameter

Field	Supported	Description
id	no	because `inputs` only supports `map<id, type \| CommandInputParameter>`
label	no
secondaryFiles	no
streamable	no
doc	yes
outputBinding	yes
format	no
type	partly	only `string`, `CWLType`, where `CWLType` is one of `File`, `Directory`