WfExS-backend stage definition

Type: object

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

No Additional Properties

The optional TRS endpoing

Type: string

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

Must be at least 1 characters long

Workflow version

Type: string or integer

If trsenpoint key is set, it will tell the version of the workflowid to look for at GA4GH TRS

A friendly nickname (prefix) for the instances

Type: string

Type: boolean Default: false

The optional, forced workflow type

Type: string

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

Type: object

Type: boolean

Container technology type to be used for this workflow

Type: enum (of string)

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"

Type: boolean Default: false

Type: object

Type: string Default: "19.04.1"

Must be at least 1 characters long

Retries in docker mode

Type: integer Default: 5

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

Value must be greater or equal to 0

(deprecated) Max number of CPUs


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

Type: integer Default: 4

Value must be greater or equal to 1

(deprecated) Max number of CPUs


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

Type: integer Default: 4

Value must be greater or equal to 1

Max task duration


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

Type: string
Must match regular expression: ^[0-9]+.*$


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

Type: string
Must match regular expression: ^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$

Must be at least 1 characters long

Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

Type: string
Must match regular expression: ^[^,]+$

Must be at least 1 characters long

Type: object

Type: string Default: "3.1.20210628163208"

Must be at least 1 characters long

Type: object

Each additional property must conform to the following schema

Type: number, integer or string

Type: object
No Additional Properties

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^(?!c-l-a-s-s)[^:;]+$
Type: object

Type: string, number or boolean
Type: array of string
No Additional Items

Each item of this array must be:

Type: array of number
No Additional Items

Each item of this array must be:

Type: array of boolean
No Additional Items

Each item of this array must be:

Type: object
No Additional Properties

Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

The following properties are required:

  • url

Type: enum (of string)

Must be one of:

  • "Directory"
  • "File"

Must not be:

Type: object

The following properties are required:

  • value
  • tabular
  • autoFill
  • autoPrefix
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

The following properties are required:

  • url

Type: const
Specific value: "ContentWithURIs"

Must not be:

Type: object

The following properties are required:

  • value
  • autoFill
  • autoPrefix
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

The following properties are required:

  • autoFill

Type: enum (of string)

Must be one of:

  • "Directory"
  • "File"

Must not be:

Type: object

The following properties are required:

  • value
  • tabular
  • url
  • secondary-urls
  • security-context
  • globExplode
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

Type: const
Specific value: "Directory"

Must not be:

Type: object

The following properties are required:

  • value
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

The following properties are required:

  • value

Type: const
Specific value: "File"

Must not be:

Type: object

The following properties are required:

  • url
  • tabular
  • secondary-urls
  • security-context
  • globExplode
  • autoFill
  • autoPrefix
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

The following properties are required:

  • value

Type: const
Specific value: "ContentWithURIs"

Must not be:

Type: object

The following properties are required:

  • url
  • secondary-urls
  • security-context
  • globExplode
  • autoFill
  • autoPrefix
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

Type: const
Specific value: "Value"

Must not be:

Type: object

The following properties are required:

  • tabular
  • url
  • secondary-urls
  • preferred-name
  • relative-dir
  • security-context
  • globExplode
  • autoFill
  • autoPrefix
  • cacheable
  • clonable

The following properties are required:

  • value
Type: object

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

Type: const
Specific value: "ContentWithURIs"

Must not be:

Type: object

The following properties are required:

  • globExplode
  • autoFill
  • autoPrefix

If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.

Type: object

The following properties are required:

  • url

Must not be:

Type: object

The following properties are required:

  • value

Must not be:

Type: object

The following properties are required:

  • url
  • secondary-urls
  • security-context

The following properties are required:

  • value

The following properties are required:

  • tabular

Type: enum (of string)

Must be one of:

  • "File"
  • "Directory"
  • "Value"
  • "ContentWithURIs"


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

Type: string

Must be at least 1 characters long

Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

Type: string

Must be at least 1 characters long

Type: object

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

Type: array of integer

The columns where URIs to be fetched are found

Must contain a minimum of 1 items

All items must be unique

No Additional Items

Each item of this array must be:

Type: enum (of string) Default: "\n"

The string used to split the tabulated content by rows

Must be one of:

  • "\n"
  • "\r"
  • "\t\n"

Type: string

The regular expression used to split the tabulated content by columns

Must be at least 1 characters long

Type: integer Default: 0

How many header rows should be skipped?

Type: object

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

Type: string
Must match regular expression: $\{[^}]+\}

Must be at least 1 characters long

Type: object
No Additional Properties

Type: array
No Additional Items

Each item of this array must be:

Type: string Default: "https://choosealicense.com/no-permission/"

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

Must be at least 1 characters long

Type: array of object

All items must be unique

No Additional Items

Each item of this array must be:

Type: object

Type: string

Name of the author

Must be at least 1 characters long

Type: string

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

Same definition as trs_endpoint

Type: array of enum (of string)

Must contain a minimum of 1 items

All items must be unique

No Additional Items

Each item of this array must be:

Type: enum (of string)

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"

Type: string
Must match regular expression: ^[^:;]+$

Must be at least 1 characters long

Type: array

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:


Type: object

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

Same definition as url

Type: boolean or string Default: false

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

Type: boolean or string Default: false

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

Type: string

Use an explicitly named security context

Must be at least 1 characters long

Type: boolean Default: true

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

Type: boolean Default: true

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

Type: boolean Default: true

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

Type: string

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

Type: boolean Default: false

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

Type: boolean Default: false

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


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

Type: string
Must match regular expression: ^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$

Must be at least 1 characters long

Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

Type: string
Must match regular expression: ^[^,]+$

Must be at least 1 characters long

Type: object
No Additional Properties

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^=\0]+$
Type: object

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

Type: object

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^:;]+$
Type: object
No Additional Properties

Type: enum (of string)

Must be one of:

  • "File"
  • "Directory"

Output cardinality

Default: 1

Expected cardinality of this output

Type: enum (of string)

Must be one of:

  • "1"
  • "?"
  • "*"
  • "+"
Type: integer

Value must be greater or equal to 0

Type: array

Must contain a minimum of 2 items

Must contain a maximum of 2 items

No Additional Items

Tuple Validation

Item at 1 must be:
Type: integer

Value must be greater or equal to 0

Item at 2 must be:
Type: integer

Value must be greater or equal to 1

Type: string

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

Must be at least 1 characters long

Type: string

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)

Must be at least 1 characters long

Type: boolean

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

Type: string

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)

Must be at least 1 characters long

Type: array
No Additional Items