WfExS-backend stage definition file (EOSC-Life Demonstrator 7 JSON Schemas)
No Additional PropertiesIf 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
If trsenpoint key is set, it will tell the version of the workflowid to look for at GA4GH TRS
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 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 at least 1
characters long
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
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
Value must be greater or equal to 1
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
Value must be greater or equal to 1
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
^[0-9]+.*$
(deprecated) If defined, the profile/s to enable
^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$
Must be at least 1
characters long
Must contain a minimum of 1
items
^[^,]+$
Must be at least 1
characters long
Must be at least 1
characters long
Each additional property must conform to the following schema
Type: number, integer or stringAll properties whose name matches the following regular expression must respect the following conditions
Property name regular expression:^(?!c-l-a-s-s)[^:;]+$
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.
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.
"ContentWithURIs"
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.
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.
"Directory"
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.
"File"
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.
"ContentWithURIs"
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.
"Value"
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.
"ContentWithURIs"
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.
When 'c-l-a-s-s' is a single file or a value, the assigned value
Must be at least 1
characters long
Must contain a minimum of 1
items
Must be at least 1
characters long
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
The columns where URIs to be fetched are found
Must contain a minimum of 1
items
All items must be unique
No Additional ItemsThe string used to split the tabulated content by rows
The regular expression used to split the tabulated content by columns
Must be at least 1
characters long
How many header rows should be skipped?
The URL(s) / URI(s) where this input is available
$\{[^}]+\}
Must be at least 1
characters long
The URI of the resource
URL to the description of the licence of the data. And by default, no permission to use or distribute it
Must be at least 1
characters long
All items must be unique
No Additional ItemsName of the author
Must be at least 1
characters long
A unique way to represent this author, either through her/his ORCID or another permanent, representative link
Same definition as trs_endpointMust contain a minimum of 1
items
All items must be unique
No Additional Items^[^:;]+$
Must be at least 1
characters long
Must contain a minimum of 1
items
This element is an array of alternate URLs, so any of them provide the very same resources
Must contain a minimum of 2
items
Secondary URLs / URIs are pointing to contents which will feed secondary inputs (CWL concept)
Same definition as urlPreferred base name / relative path for this input, instead of the derived one from the URL
Put contents fetched for this input in this relative directory. This option does not affect preferred-name
Use an explicitly named security context
Must be at least 1
characters long
Whether this input contents can be included in RO-Crates or exported
Whether a copy of this input contents can be kept locally outside the working directory
Whether a copy of this input contents can be kept locally inside the working directory
When this is set, and the class is directory, it helps filtering in what it should be included
When this key is true, the directory or file is considered an output one
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
^[^, ]+[ ]*(,[ ]*[^, ]+[ ]*)*$
Must be at least 1
characters long
Must contain a minimum of 1
items
^[^,]+$
Must be at least 1
characters long
All properties whose name matches the following regular expression must respect the following conditions
Property name regular expression:^[^=\0]+$
The name of an environment variable. These names cannot contain either the equal or the character \0
All properties whose name matches the following regular expression must respect the following conditions
Property name regular expression:^[^:;]+$
Expected cardinality of this output
Value must be greater or equal to 0
Must contain a minimum of 2
items
Must contain a maximum of 2
items
Value must be greater or equal to 0
Value must be greater or equal to 1
Preferred name for this output, honored when either filledFrom or glob are used
Must be at least 1
characters long
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
Is this output a synthetic one? The default value when it is not defined depends on the type of workflow.
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