WfExS-backend stage definition

Contents

WfExS-backend stage definition#

Title: WfExS-backend stage definition

Type

object

Required

No

Additional properties

[Not allowed]

Description: WfExS-backend stage definition file (EOSC-Life Demonstrator 7 JSON Schemas)

Property

Pattern

Type

Deprecated

Definition

Title/Description

- trs_endpoint

No

string

No

In #/definitions/PlainURI

The optional TRS endpoing

- version

No

string or integer

No

-

Workflow version

+ workflow_id

No

Combination

No

-

-

- nickname

No

string

No

-

A friendly nickname (prefix) for the instances

- paranoid_mode

No

boolean

No

-

-

- workflow_type

No

string

No

-

The optional, forced workflow type

- workflow_config

No

object

No

-

-

- placeholders

No

object

No

-

-

- params

No

object

No

In #/definitions/Params

-

- profile

No

Combination

No

-

For engines which support profiles, like Nextflow or snakemake, if defined, the profile/s to enable

- environment

No

object

No

-

-

- outputs

No

object

No

-

-

- default_actions

No

array

No

-

-

1. Property WfExS-backend stage definition > trs_endpoint#

Title: The optional TRS endpoing

Type

string

Required

No

Defined in

#/definitions/PlainURI

Description: If this key is set, it will tell the GA4GH TRS service where to look for the workflow_id (and optional version)

Restrictions

Min length

1

2. Property WfExS-backend stage definition > version#

Title: Workflow version

Type

string or integer

Required

No

Description: If trs_enpoint key is set, it will tell the version of the workflow_id to look for at GA4GH TRS

3. Property WfExS-backend stage definition > workflow_id#

Type

combining

Required

Yes

Additional properties

[Any type: allowed]

Any of(Option)

PlainURI

item 1

item 2

3.1. Property WfExS-backend stage definition > workflow_id > anyOf > PlainURI#

Type

string

Required

No

Same definition as

trs_endpoint

3.2. Property WfExS-backend stage definition > workflow_id > anyOf > item 1#

Type

string

Required

No

3.3. Property WfExS-backend stage definition > workflow_id > anyOf > item 2#

Type

integer

Required

No

4. Property WfExS-backend stage definition > nickname#

Title: A friendly nickname (prefix) for the instances

Type

string

Required

No

5. Property WfExS-backend stage definition > paranoid_mode#

Type

boolean

Required

No

Default

false

6. Property WfExS-backend stage definition > workflow_type#

Title: The optional, forced workflow type

Type

string

Required

No

Description: When this key is set, it is forcing the workflow type. WfExS-backend is usually able to identify the workflow type, unless there are two intertwined workflows in the same location

7. Property WfExS-backend stage definition > workflow_config#

Type

object

Required

No

Additional properties

[Any type: allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

- secure

No

boolean

No

-

-

- containerType

No

enum (of string)

No

-

Container technology type to be used for this workflow

- writable_containers

No

boolean

No

-

-

- nextflow

No

object

No

-

-

- cwl

No

object

No

-

-

7.1. Property WfExS-backend stage definition > workflow_config > secure#

Type

boolean

Required

No

7.2. Property WfExS-backend stage definition > workflow_config > containerType#

Title: Container technology type to be used for this workflow

Type

enum (of string)

Required

No

Description: Type of container technology to be used when this staging scenario is instantiated. Supported types are:

  • Singularity (default).

  • Docker.

  • Podman

  • No containerisation technology (discouraged, but needed for some workflows) Encrypted working directories are unsupported when Docker or Podman are used due technological limitations

Must be one of:

  • “singularity”

  • “docker”

  • “podman”

  • “none”

7.3. Property WfExS-backend stage definition > workflow_config > writable_containers#

Type

boolean

Required

No

Default

false

7.4. Property WfExS-backend stage definition > workflow_config > nextflow#

Type

object

Required

No

Additional properties

[Any type: allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

- version

No

string

No

-

-

- maxRetries

No

integer

No

-

Retries in docker mode

- maxProcesses

No

Combination

No

-

(deprecated) Max number of CPUs

- maxCPUs

No

Combination

No

-

(deprecated) Max number of CPUs

- maxTaskDuration

No

Combination

No

-

Max task duration

- profile

No

Combination

No

-

(deprecated) If defined, the profile/s to enable

7.4.1. Property WfExS-backend stage definition > workflow_config > nextflow > version#

Type

string

Required

No

Default

"19.04.1"

Restrictions

Min length

1

7.4.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxRetries#

Title: Retries in docker mode

Type

integer

Required

No

Default

5

Description: Retries when engineMode is docker. Retries system was introduced when using docker-in-docker pattern because an insidious bug happens sometimes. See https://forums.docker.com/t/any-known-problems-with-symlinks-on-bind-mounts/32138

Restrictions

Minimum

≥ 0

7.4.3. Property WfExS-backend stage definition > workflow_config > nextflow > maxProcesses#

Title: (deprecated) Max number of CPUs

Type

combining

Required

No

Additional properties

[Any type: allowed]

Description: Number of CPUs to be used by Nextflow. When this key has an explicit value of null, it depends on Nextflow criteria, which tries creating as many processes as available CPUs, spawning jobs in parallel. Not declaring it, or declaring and explicit value, imposes a limitation in the number of concurrent processes

One of(Option)

item 0

item 1

7.4.3.1. Property WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 0#

Type

integer

Required

No

Default

4

Restrictions

Minimum

≥ 1

7.4.3.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 1#

Type

null

Required

No

7.4.4. Property WfExS-backend stage definition > workflow_config > nextflow > maxCPUs#

Title: (deprecated) Max number of CPUs

Type

combining

Required

No

Additional properties

[Any type: allowed]

Description: Number of CPUs to be used by Nextflow. When this key has an explicit value of null, it depends on Nextflow criteria, which tries creating as many processes as available CPUs, spawning jobs in parallel. Not declaring it, or declaring and explicit value, imposes a limitation in the number of concurrent processes

One of(Option)

item 0

item 1

7.4.4.1. Property WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 0#

Type

integer

Required

No

Default

4

Restrictions

Minimum

≥ 1

7.4.4.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 1#

Type

null

Required

No

7.4.5. Property WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration#

Title: Max task duration

Type

combining

Required

No

Additional properties

[Any type: allowed]

Description: With this parameter it is possible to override the max task time declared for processes. This is needed for workflows which are not so customizable

One of(Option)

item 0

item 1

7.4.5.1. Property WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 0#

Type

string

Required

No

Restrictions

Must match regular expression

^[0-9]+.*$ Test

7.4.5.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 1#

Type

null

Required

No

7.4.6. Property WfExS-backend stage definition > workflow_config > nextflow > profile#

Type

combining

Required

No

Additional properties

[Any type: allowed]

Description: (deprecated) If defined, the profile/s to enable

One of(Option)

item 0

item 1

7.4.6.1. Property WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 0#

Type

string

Required

No

Restrictions

Min length

1

Must match regular expression

^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$ Test

7.4.6.2. Property WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1#

Type

array of string

Required

No

Array restrictions

Min items

1

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 1 items

-

7.4.6.2.1. WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1 > item 1 items#

Type

string

Required

No

Restrictions

Min length

1

Must match regular expression

^[^,]+$ Test

7.5. Property WfExS-backend stage definition > workflow_config > cwl#

Type

object

Required

No

Additional properties

[Any type: allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

- version

No

string

No

-

-

7.5.1. Property WfExS-backend stage definition > workflow_config > cwl > version#

Type

string

Required

No

Default

"3.1.20210628163208"

Restrictions

Min length

1

8. Property WfExS-backend stage definition > placeholders#

Type

object

Required

No

Additional properties

[Should-conform]

Property

Pattern

Type

Deprecated

Definition

Title/Description

- placeholders_additionalProperties

No

number, integer or string

No

-

-

8.1. Property WfExS-backend stage definition > placeholders > additionalProperties#

Type

number, integer or string

Required

No

9. Property WfExS-backend stage definition > params#

Type

object

Required

No

Additional properties

[Not allowed]

Defined in

#/definitions/Params

Property

Pattern

Type

Deprecated

Definition

Title/Description

- [^(?!c-l-a-s-s)[^:;]+$](#params_pattern1 )

Yes

object

No

In #/definitions/Param

-

9.1. Pattern Property WfExS-backend stage definition > params > Param#

All properties whose name matches the regular expression ^(?!c-l-a-s-s)[^:;]+$ (Test) must respect the following conditions

Type

combining

Required

No

Additional properties

[Any type: allowed]

Defined in

#/definitions/Param

9.1.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 0#

Type

string, number or boolean

Required

No

9.1.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1#

Type

array of string

Required

No

Array restrictions

Min items

N/A

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 1 items

-

9.1.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1 > item 1 items#

Type

string

Required

No

9.1.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2#

Type

array of number

Required

No

Array restrictions

Min items

N/A

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 2 items

-

9.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2 > item 2 items#

Type

number

Required

No

9.1.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3#

Type

array of boolean

Required

No

Array restrictions

Min items

N/A

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 3 items

-

9.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3 > item 3 items#

Type

boolean

Required

No

9.1.5. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > DirFile#

Type

combining

Required

No

Additional properties

[Not allowed]

Defined in

#/definitions/DirFile

Property

Pattern

Type

Deprecated

Definition

Title/Description

+ c-l-a-s-s

No

enum (of string)

No

-

-

- value

No

Combination

No

-

When ‘c-l-a-s-s’ is a single file or a value, the assigned value

- tabular

No

object

No

-

When it is content with URIs, we are telling it is a tabular one with this key. URIs are fetched, and the absolute paths replace them in the generated content tab

- url

No

object

No

In #/definitions/InputURI

The URL(s) / URI(s) where this input is available

- secondary-urls

No

object

No

Same as url

Secondary URLs / URIs are pointing to contents which will feed secondary inputs (CWL concept)

- preferred-name

No

boolean or string

No

-

Preferred base name / relative path for this input, instead of the derived one from the URL

- relative-dir

No

boolean or string

No

-

Put contents fetched for this input in this relative directory. This option does not affect preferred-name

- security-context

No

string

No

-

Use an explicitly named security context

- disclosable

No

boolean

No

-

Whether this input contents can be included in RO-Crates or exported

- cacheable

No

boolean

No

-

Whether a copy of this input contents can be kept locally outside the working directory

- clonable

No

boolean

No

-

Whether a copy of this input contents can be kept locally inside the working directory

- globExplode

No

string

No

-

When this is set, and the class is directory, it helps filtering in what it should be included

- autoFill

No

boolean

No

-

When this key is true, the directory or file is considered an output one

- autoPrefix

No

boolean

No

-

When autoFill is true and this parameter is false, this directory is mapped to the parent output one for this execution. When both autoFill and this parameter are true, an output file or directory name is assigned, based on its complete param name

9.1.5.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 0#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.1.1. If (c-l-a-s-s = Must be one of:#
  • “Directory”

  • “File” )

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.1.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.1.1.1.1. The following properties are required#
  • value

  • tabular

  • autoFill

  • autoPrefix

9.1.5.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 1#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.2.1. If (c-l-a-s-s = “ContentWithURIs” )#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.2.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.2.1.1.1. The following properties are required#
  • value

  • autoFill

  • autoPrefix

9.1.5.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 2#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.3.1. If (c-l-a-s-s = Must be one of:#
  • “Directory”

  • “File” )

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.3.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.3.1.1.1. The following properties are required#
  • value

  • tabular

  • url

  • secondary-urls

  • security-context

  • globExplode

9.1.5.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 3#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.4.1. If (c-l-a-s-s = “Directory” )#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.4.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.4.1.1.1. The following properties are required#
  • value

9.1.5.5. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 4#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.5.1. If (c-l-a-s-s = “File” )#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.5.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.5.1.1.1. The following properties are required#
  • url

  • tabular

  • secondary-urls

  • security-context

  • globExplode

  • autoFill

  • autoPrefix

9.1.5.6. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 5#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.6.1. If (c-l-a-s-s = “ContentWithURIs” )#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.6.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.6.1.1.1. The following properties are required#
  • url

  • secondary-urls

  • security-context

  • globExplode

  • autoFill

  • autoPrefix

9.1.5.7. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 6#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.7.1. If (c-l-a-s-s = “Value” )#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.7.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.7.1.1.1. The following properties are required#
  • tabular

  • url

  • secondary-urls

  • preferred-name

  • relative-dir

  • security-context

  • globExplode

  • autoFill

  • autoPrefix

  • cacheable

  • clonable

9.1.5.7.1.2. The following properties are required#
  • value

9.1.5.8. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 7#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1. If (c-l-a-s-s = “ContentWithURIs” )#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1.1. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1.1.1. The following properties are required#
  • globExplode

  • autoFill

  • autoPrefix

          If(_complex condition_)
    

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1.1.2. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1.1.2.1. The following properties are required#
  • value

          IfNot(_complex condition_)
    

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1.1.3. Must not be#

Type

object

Required

No

Additional properties

[Any type: allowed]

9.1.5.8.1.1.3.1. The following properties are required#
  • url

  • secondary-urls

  • security-context

9.1.5.8.1.1.4. The following properties are required#
  • value

9.1.5.8.1.2. The following properties are required#
  • tabular

9.1.5.9. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > c-l-a-s-s#

Type

enum (of string)

Required

Yes

Must be one of:

  • “File”

  • “Directory”

  • “Value”

  • “ContentWithURIs”

9.1.5.10. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value#

Type

combining

Required

No

Additional properties

[Any type: allowed]

Description: When ‘c-l-a-s-s’ is a single file or a value, the assigned value

One of(Option)

item 0

item 1

9.1.5.10.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 0#

Type

string

Required

No

Restrictions

Min length

1

9.1.5.10.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1#

Type

array of string

Required

No

Array restrictions

Min items

1

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 1 items

-

9.1.5.10.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1 > item 1 items#

Type

string

Required

No

Restrictions

Min length

1

9.1.5.11. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular#

Type

object

Required

No

Additional properties

[Any type: allowed]

Description: When it is content with URIs, we are telling it is a tabular one with this key. URIs are fetched, and the absolute paths replace them in the generated content tab

Property

Pattern

Type

Deprecated

Definition

Title/Description

+ uri-columns

No

array of integer

No

-

The columns where URIs to be fetched are found

- row-sep

No

enum (of string)

No

-

The string used to split the tabulated content by rows

+ column-sep

No

string

No

-

The regular expression used to split the tabulated content by columns

- header-rows

No

integer

No

-

How many header rows should be skipped?

9.1.5.11.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns#

Type

array of integer

Required

Yes

Description: The columns where URIs to be fetched are found

Array restrictions

Min items

1

Max items

N/A

Items unicity

True

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

uri-columns items

-

9.1.5.11.1.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns > uri-columns items#

Type

integer

Required

No

9.1.5.11.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > row-sep#

Type

enum (of string)

Required

No

Default

"\n"

Description: The string used to split the tabulated content by rows

Must be one of:

  • “\n”

  • “\r”

  • “\t\n”

Restrictions

Min length

1

9.1.5.11.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > column-sep#

Type

string

Required

Yes

Description: The regular expression used to split the tabulated content by columns

Restrictions

Min length

1

9.1.5.11.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > header-rows#

Type

integer

Required

No

Default

0

Description: How many header rows should be skipped?

9.1.5.12. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url#

Type

combining

Required

No

Additional properties

[Any type: allowed]

Defined in

#/definitions/InputURI

Description: The URL(s) / URI(s) where this input is available

9.1.5.12.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlainURI#

Type

string

Required

No

Same definition as

trs_endpoint

9.1.5.12.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlaceholderURI#

Type

string

Required

No

Defined in

#/definitions/PlaceholderURI

Restrictions

Min length

1

Must match regular expression

$\{[^}]+\} Test

9.1.5.12.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > LicensedURI#

Type

object

Required

No

Additional properties

[Not allowed]

Defined in

#/definitions/LicensedURI

Property

Pattern

Type

Deprecated

Definition

Title/Description

+ uri

No

Combination

No

-

The URI of the resource

- licences

No

array

No

-

-

- attributions

No

array of object

No

-

-

- security-context

No

string

No

-

-

9.1.5.12.3.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri#

Type

combining

Required

Yes

Additional properties

[Any type: allowed]

Description: The URI of the resource

Any of(Option)

PlainURI

PlaceholderURI

9.1.5.12.3.1.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlainURI#

Type

string

Required

No

Same definition as

trs_endpoint

9.1.5.12.3.1.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlaceholderURI#

Type

string

Required

No

Same definition as

params_pattern1_pattern1_i4_url_oneOf_i1

9.1.5.12.3.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences#

Type

array

Required

No

Array restrictions

Min items

N/A

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

PlainURI

URL to the description of the licence of the data. And by default, no permission to use or distribute it

9.1.5.12.3.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences > PlainURI#

Type

string

Required

No

Default

"https://choosealicense.com/no-permission/"

Defined in

#/definitions/PlainURI

Description: URL to the description of the licence of the data. And by default, no permission to use or distribute it

Restrictions

Min length

1

9.1.5.12.3.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions#

Type

array of object

Required

No

Array restrictions

Min items

N/A

Max items

N/A

Items unicity

True

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

attributions items

-

9.1.5.12.3.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items#

Type

object

Required

No

Additional properties

[Any type: allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

+ name

No

string

No

-

Name of the author

+ pid

No

string

No

Same as trs_endpoint

A unique way to represent this author, either through her/his ORCID or another permanent, representative link

+ roles

No

array of enum (of string)

No

-

-

9.1.5.12.3.3.1.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > name#

Type

string

Required

Yes

Description: Name of the author

Restrictions

Min length

1

9.1.5.12.3.3.1.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > pid#

Type

string

Required

Yes

Same definition as

trs_endpoint

Description: A unique way to represent this author, either through her/his ORCID or another permanent, representative link

9.1.5.12.3.3.1.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles#

Type

array of enum (of string)

Required

Yes

Array restrictions

Min items

1

Max items

N/A

Items unicity

True

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

roles items

-

9.1.5.12.3.3.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles > roles items#

Type

enum (of string)

Required

No

Must be one of:

  • “conceptualization”

  • “data-curation”

  • “formal-analysis”

  • “funding-acquisition”

  • “investigation”

  • “methodology”

  • “project-administration”

  • “resources”

  • “software”

  • “supervision”

  • “validation”

  • “visualization”

  • “writing-original-draft”

  • “writing-review-editing”

9.1.5.12.3.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > security-context#

Type

string

Required

No

Restrictions

Min length

1

Must match regular expression

^[^:;]+$ Test

9.1.5.12.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3#

Type

array

Required

No

Array restrictions

Min items

1

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 3 items

-

9.1.5.12.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.12.4.1.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > LicensedURI#

Type

object

Required

No

Additional properties

[Not allowed]

Same definition as

params_pattern1_pattern1_i4_url_oneOf_i2

9.1.5.12.4.1.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlainURI#

Type

string

Required

No

Same definition as

trs_endpoint

9.1.5.12.4.1.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI#

Type

string

Required

No

Same definition as

params_pattern1_pattern1_i4_url_oneOf_i1

9.1.5.12.4.1.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3#

Type

array

Required

No

Description: This element is an array of alternate URLs, so any of them provide the very same resources

Array restrictions

Min items

2

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 3 items

-

9.1.5.12.4.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items#

Type

combining

Required

No

Additional properties

[Any type: allowed]

9.1.5.12.4.1.4.1.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > LicensedURI#

Type

object

Required

No

Additional properties

[Not allowed]

Same definition as

params_pattern1_pattern1_i4_url_oneOf_i2

9.1.5.12.4.1.4.1.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > PlainURI#

Type

string

Required

No

Same definition as

trs_endpoint

9.1.5.12.4.1.4.1.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI#

Type

string

Required

No

Same definition as

params_pattern1_pattern1_i4_url_oneOf_i1

9.1.5.13. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > secondary-urls#

Type

combining

Required

No

Additional properties

[Any type: allowed]

Same definition as

url

Description: Secondary URLs / URIs are pointing to contents which will feed secondary inputs (CWL concept)

9.1.5.14. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > preferred-name#

Type

boolean or string

Required

No

Default

false

Description: Preferred base name / relative path for this input, instead of the derived one from the URL

Restrictions

Min length

1

9.1.5.15. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > relative-dir#

Type

boolean or string

Required

No

Default

false

Description: Put contents fetched for this input in this relative directory. This option does not affect preferred-name

Restrictions

Min length

1

9.1.5.16. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > security-context#

Type

string

Required

No

Description: Use an explicitly named security context

Restrictions

Min length

1

9.1.5.17. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > disclosable#

Type

boolean

Required

No

Default

true

Description: Whether this input contents can be included in RO-Crates or exported

9.1.5.18. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > cacheable#

Type

boolean

Required

No

Default

true

Description: Whether a copy of this input contents can be kept locally outside the working directory

9.1.5.19. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > clonable#

Type

boolean

Required

No

Default

true

Description: Whether a copy of this input contents can be kept locally inside the working directory

9.1.5.20. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > globExplode#

Type

string

Required

No

Description: When this is set, and the class is directory, it helps filtering in what it should be included

9.1.5.21. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoFill#

Type

boolean

Required

No

Default

false

Description: When this key is true, the directory or file is considered an output one

9.1.5.22. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoPrefix#

Type

boolean

Required

No

Default

false

Description: When autoFill is true and this parameter is false, this directory is mapped to the parent output one for this execution. When both autoFill and this parameter are true, an output file or directory name is assigned, based on its complete param name

9.1.6. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > Params#

Type

object

Required

No

Additional properties

[Not allowed]

Same definition as

params

10. Property WfExS-backend stage definition > profile#

Type

combining

Required

No

Additional properties

[Any type: allowed]

Description: For engines which support profiles, like Nextflow or snakemake, if defined, the profile/s to enable

One of(Option)

item 0

item 1

10.1. Property WfExS-backend stage definition > profile > oneOf > item 0#

Type

string

Required

No

Restrictions

Min length

1

Must match regular expression

^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$ Test

10.2. Property WfExS-backend stage definition > profile > oneOf > item 1#

Type

array of string

Required

No

Array restrictions

Min items

1

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 1 items

-

10.2.1. WfExS-backend stage definition > profile > oneOf > item 1 > item 1 items#

Type

string

Required

No

Restrictions

Min length

1

Must match regular expression

^[^,]+$ Test

11. Property WfExS-backend stage definition > environment#

Type

object

Required

No

Additional properties

[Not allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

- [^[^=\0]+$](#environment_pattern1 )

Yes

object

No

In #/definitions/EnvVar

The name of an environment variable. These names cannot contain either the equal or the character \0

11.1. Pattern Property WfExS-backend stage definition > environment > EnvVar#

All properties whose name matches the regular expression ^[^=\0]+$ (Test) must respect the following conditions

Type

combining

Required

No

Additional properties

[Any type: allowed]

Defined in

#/definitions/EnvVar

Description: The name of an environment variable. These names cannot contain either the equal or the character \0

One of(Option)

item 0

DirFile

11.1.1. Property WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > item 0#

Type

string or number

Required

No

11.1.2. Property WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > DirFile#

Type

combining

Required

No

Additional properties

[Not allowed]

Same definition as

params_pattern1_pattern1_i4

12. Property WfExS-backend stage definition > outputs#

Type

object

Required

No

Additional properties

[Any type: allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

- [^[^:;]+$](#outputs_pattern1 )

Yes

object

No

-

-

12.1. Pattern Property WfExS-backend stage definition > outputs > ^[^:;]+$#

All properties whose name matches the regular expression ^[^:;]+$ (Test) must respect the following conditions

Type

object

Required

No

Additional properties

[Not allowed]

Property

Pattern

Type

Deprecated

Definition

Title/Description

+ c-l-a-s-s

No

enum (of string)

No

-

-

- cardinality

No

Combination

No

-

Output cardinality

- preferredName

No

string

No

-

Preferred name for this output, honored when either filledFrom or glob are used

- fillFrom

No

string

No

-

Autofilled input from where to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake)

- syntheticOutput

No

boolean

No

-

Is this output a synthetic one? The default value when it is not defined depends on the type of workflow.

- glob

No

string

No

-

Glob pattern to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake)

12.1.1. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > c-l-a-s-s#

Type

enum (of string)

Required

Yes

Must be one of:

  • “File”

  • “Directory”

12.1.2. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality#

Title: Output cardinality

Type

combining

Required

No

Additional properties

[Any type: allowed]

Default

1

Description: Expected cardinality of this output

One of(Option)

item 0

item 1

item 2

12.1.2.1. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 0#

Type

enum (of string)

Required

No

Must be one of:

  • “1”

  • “?”

  • “*”

  • “+”

12.1.2.2. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 1#

Type

integer

Required

No

Restrictions

Minimum

≥ 0

12.1.2.3. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2#

Type

array

Required

No

Array restrictions

Min items

2

Max items

2

Items unicity

False

Additional items

False

Tuple validation

See below

Each item of this array must be

Description

item 2 item 0

-

item 2 item 1

-

12.1.2.3.1. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 0#

Type

integer

Required

No

Restrictions

Minimum

≥ 0

12.1.2.3.2. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 1#

Type

integer

Required

No

Restrictions

Minimum

≥ 1

12.1.3. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > preferredName#

Type

string

Required

No

Description: Preferred name for this output, honored when either filledFrom or glob are used

Restrictions

Min length

1

12.1.4. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > fillFrom#

Type

string

Required

No

Description: Autofilled input from where to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake)

Restrictions

Min length

1

12.1.5. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > syntheticOutput#

Type

boolean

Required

No

Description: Is this output a synthetic one? The default value when it is not defined depends on the type of workflow.

12.1.6. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > glob#

Type

string

Required

No

Description: Glob pattern to get the files and directories to be assigned to this output, useful in workflow models where outputs are not explicitly declared (Nextflow, Snakemake)

Restrictions

Min length

1

13. Property WfExS-backend stage definition > default_actions#

Type

array

Required

No

Array restrictions

Min items

N/A

Max items

N/A

Items unicity

False

Additional items

False

Tuple validation

N/A


Generated using json-schema-for-humans on 2024-12-03 at 23:43:14 +0000