WfExS-backend stage definition#
7. Property
WfExS-backend stage definition > workflow_config
7.1. Property
WfExS-backend stage definition > workflow_config > secure
7.2. Property
WfExS-backend stage definition > workflow_config > containerType
7.3. Property
WfExS-backend stage definition > workflow_config > writable_containers
7.4. Property
WfExS-backend stage definition > workflow_config > nextflow
7.4.1. Property
WfExS-backend stage definition > workflow_config > nextflow > version
7.4.2. Property
WfExS-backend stage definition > workflow_config > nextflow > maxRetries
7.4.3. Property
WfExS-backend stage definition > workflow_config > nextflow > maxProcesses
7.4.4. Property
WfExS-backend stage definition > workflow_config > nextflow > maxCPUs
7.4.5. Property
WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration
7.4.6. Property
WfExS-backend stage definition > workflow_config > nextflow > profile
7.5. Property
WfExS-backend stage definition > workflow_config > cwl
9. Property
WfExS-backend stage definition > params
9.1. Pattern Property
WfExS-backend stage definition > params > Param
9.1.1. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 0
9.1.2. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1
[9.1.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1 > item 1 items](#autogenerated_heading_3)
9.1.3. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2
[9.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2 > item 2 items](#autogenerated_heading_4)
9.1.4. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3
[9.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3 > item 3 items](#autogenerated_heading_5)
9.1.5. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > DirFile
-
[9.1.5.1.1. If (c-l-a-s-s = Must be one of:
-
“Directory”
“File” )](#autogenerated_heading_6) - 9.1.5.1.1.1. Must not be - 9.1.5.1.1.1.1. The following properties are required - 9.1.5.2. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 1
- 9.1.5.2.1. If (c-l-a-s-s = “ContentWithURIs” ) - 9.1.5.2.1.1. Must not be - 9.1.5.2.1.1.1. The following properties are required - 9.1.5.3. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 2
- [9.1.5.3.1. If (c-l-a-s-s = Must be one of:“Directory”
“File” )](#autogenerated_heading_12) - 9.1.5.3.1.1. Must not be - 9.1.5.3.1.1.1. The following properties are required - 9.1.5.4. Property
WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 3
- 9.1.5.4.1. If (c-l-a-s-s = “Directory” ) - 9.1.5.4.1.1. Must not be - 9.1.5.4.1.1.1. The following properties are required - 9.1.5.5. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 4
- 9.1.5.5.1. If (c-l-a-s-s = “File” ) - 9.1.5.5.1.1. Must not be - 9.1.5.5.1.1.1. The following properties are required - 9.1.5.6. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 5
- 9.1.5.6.1. If (c-l-a-s-s = “ContentWithURIs” ) - 9.1.5.6.1.1. Must not be - 9.1.5.6.1.1.1. The following properties are required - 9.1.5.7. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 6
- 9.1.5.7.1. If (c-l-a-s-s = “Value” ) - 9.1.5.7.1.1. Must not be - 9.1.5.7.1.1.1. The following properties are required - 9.1.5.7.1.2. The following properties are required - 9.1.5.8. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > allOf > item 7
- 9.1.5.8.1. If (c-l-a-s-s = “ContentWithURIs” ) - 9.1.5.8.1.1. Must not be - 9.1.5.8.1.1.1. The following properties are required - 9.1.5.8.1.1.2. Must not be - 9.1.5.8.1.1.2.1. The following properties are required - 9.1.5.8.1.1.3. Must not be - 9.1.5.8.1.1.3.1. The following properties are required - 9.1.5.8.1.1.4. The following properties are required - 9.1.5.8.1.2. The following properties are required - 9.1.5.9. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > c-l-a-s-s
- 9.1.5.10. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value
- 9.1.5.10.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 0
- 9.1.5.10.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 1
- [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](#autogenerated_heading_37) - 9.1.5.11. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular
- 9.1.5.11.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > uri-columns
- [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](#autogenerated_heading_38) - 9.1.5.11.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > row-sep
- 9.1.5.11.3. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > column-sep
- 9.1.5.11.4. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > tabular > header-rows
- 9.1.5.12. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url
- 9.1.5.12.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlainURI
- 9.1.5.12.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlaceholderURI
- 9.1.5.12.3. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > LicensedURI
- 9.1.5.12.3.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri
- 9.1.5.12.3.1.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlainURI
- 9.1.5.12.3.1.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > uri > anyOf > PlaceholderURI
- 9.1.5.12.3.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > licences
- [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](#autogenerated_heading_39) - 9.1.5.12.3.3. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions
- [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](#autogenerated_heading_40) - 9.1.5.12.3.3.1.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > name
- 9.1.5.12.3.3.1.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > pid
- 9.1.5.12.3.3.1.3. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > attributions > attributions items > roles
- [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](#autogenerated_heading_41) - 9.1.5.12.3.4. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 2 > security-context
- 9.1.5.12.4. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3
- [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](#autogenerated_heading_42) - 9.1.5.12.4.1.1. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > LicensedURI
- 9.1.5.12.4.1.2. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlainURI
- 9.1.5.12.4.1.3. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > PlaceholderURI
- 9.1.5.12.4.1.4. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3 > item 3 items > oneOf > item 3
- [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](#autogenerated_heading_43) - 9.1.5.12.4.1.4.1.1. PropertyWfExS-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
- 9.1.5.12.4.1.4.1.2. PropertyWfExS-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
- 9.1.5.12.4.1.4.1.3. PropertyWfExS-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
- 9.1.5.13. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > secondary-urls
- 9.1.5.14. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > preferred-name
- 9.1.5.15. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > relative-dir
- 9.1.5.16. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > security-context
- 9.1.5.17. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > disclosable
- 9.1.5.18. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > cacheable
- 9.1.5.19. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > clonable
- 9.1.5.20. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > globExplode
- 9.1.5.21. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoFill
- 9.1.5.22. PropertyWfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > autoPrefix
12. Property
WfExS-backend stage definition > outputs
12.1. Pattern Property
WfExS-backend stage definition > outputs > ^[^:;]+$
12.1.1. Property
WfExS-backend stage definition > outputs > ^[^:;]+$ > c-l-a-s-s
12.1.2. Property
WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality
12.1.3. Property
WfExS-backend stage definition > outputs > ^[^:;]+$ > preferredName
12.1.4. Property
WfExS-backend stage definition > outputs > ^[^:;]+$ > fillFrom
12.1.5. Property
WfExS-backend stage definition > outputs > ^[^:;]+$ > syntheticOutput
12.1.6. Property
WfExS-backend stage definition > outputs > ^[^:;]+$ > glob
13. Property
WfExS-backend stage definition > default_actions
Title: WfExS-backend stage definition
Type |
|
Required |
No |
Additional properties |
Description: WfExS-backend stage definition file (EOSC-Life Demonstrator 7 JSON Schemas)
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
No |
string |
No |
In #/definitions/PlainURI |
The optional TRS endpoing |
|
- version |
No |
string or integer |
No |
- |
Workflow version |
No |
Combination |
No |
- |
- |
|
- nickname |
No |
string |
No |
- |
A friendly nickname (prefix) for the instances |
No |
boolean |
No |
- |
- |
|
No |
string |
No |
- |
The optional, forced workflow type |
|
No |
object |
No |
- |
- |
|
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 |
No |
object |
No |
- |
- |
|
- outputs |
No |
object |
No |
- |
- |
No |
array |
No |
- |
- |
1. Property WfExS-backend stage definition > trs_endpoint
#
Title: The optional TRS endpoing
Type |
|
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 |
|
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 |
|
Required |
Yes |
Additional properties |
3.1. Property WfExS-backend stage definition > workflow_id > anyOf > PlainURI
#
Type |
|
Required |
No |
Same definition as |
3.2. Property WfExS-backend stage definition > workflow_id > anyOf > item 1
#
Type |
|
Required |
No |
3.3. Property WfExS-backend stage definition > workflow_id > anyOf > item 2
#
Type |
|
Required |
No |
4. Property WfExS-backend stage definition > nickname
#
Title: A friendly nickname (prefix) for the instances
Type |
|
Required |
No |
5. Property WfExS-backend stage definition > paranoid_mode
#
Type |
|
Required |
No |
Default |
|
6. Property WfExS-backend stage definition > workflow_type
#
Title: The optional, forced workflow type
Type |
|
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 |
|
Required |
No |
Additional properties |
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
- secure |
No |
boolean |
No |
- |
- |
No |
enum (of string) |
No |
- |
Container technology type to be used for this workflow |
|
No |
boolean |
No |
- |
- |
|
- nextflow |
No |
object |
No |
- |
- |
- cwl |
No |
object |
No |
- |
- |
7.1. Property WfExS-backend stage definition > workflow_config > secure
#
Type |
|
Required |
No |
7.2. Property WfExS-backend stage definition > workflow_config > containerType
#
Title: Container technology type to be used for this workflow
Type |
|
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 |
|
Required |
No |
Default |
|
7.4. Property WfExS-backend stage definition > workflow_config > nextflow
#
Type |
|
Required |
No |
Additional properties |
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
- version |
No |
string |
No |
- |
- |
No |
integer |
No |
- |
Retries in docker mode |
|
No |
Combination |
No |
- |
(deprecated) Max number of CPUs |
|
- maxCPUs |
No |
Combination |
No |
- |
(deprecated) Max number of CPUs |
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 |
|
Required |
No |
Default |
|
Restrictions |
|
---|---|
Min length |
1 |
7.4.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxRetries
#
Title: Retries in docker mode
Type |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Additional properties |
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
7.4.3.1. Property WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 0
#
Type |
|
Required |
No |
Default |
|
Restrictions |
|
---|---|
Minimum |
≥ 1 |
7.4.3.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxProcesses > oneOf > item 1
#
Type |
|
Required |
No |
7.4.4. Property WfExS-backend stage definition > workflow_config > nextflow > maxCPUs
#
Title: (deprecated) Max number of CPUs
Type |
|
Required |
No |
Additional properties |
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
7.4.4.1. Property WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 0
#
Type |
|
Required |
No |
Default |
|
Restrictions |
|
---|---|
Minimum |
≥ 1 |
7.4.4.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxCPUs > oneOf > item 1
#
Type |
|
Required |
No |
7.4.5. Property WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration
#
Title: Max task duration
Type |
|
Required |
No |
Additional properties |
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
7.4.5.1. Property WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 0
#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Must match regular expression |
|
7.4.5.2. Property WfExS-backend stage definition > workflow_config > nextflow > maxTaskDuration > oneOf > item 1
#
Type |
|
Required |
No |
7.4.6. Property WfExS-backend stage definition > workflow_config > nextflow > profile
#
Type |
|
Required |
No |
Additional properties |
Description: (deprecated) If defined, the profile/s to enable
7.4.6.1. Property WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 0
#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Min length |
1 |
Must match regular expression |
|
7.4.6.2. Property WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1
#
Type |
|
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 |
---|---|
- |
7.4.6.2.1. WfExS-backend stage definition > workflow_config > nextflow > profile > oneOf > item 1 > item 1 items#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Min length |
1 |
Must match regular expression |
|
7.5. Property WfExS-backend stage definition > workflow_config > cwl
#
Type |
|
Required |
No |
Additional properties |
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
- version |
No |
string |
No |
- |
- |
7.5.1. Property WfExS-backend stage definition > workflow_config > cwl > version
#
Type |
|
Required |
No |
Default |
|
Restrictions |
|
---|---|
Min length |
1 |
8. Property WfExS-backend stage definition > placeholders
#
Type |
|
Required |
No |
Additional properties |
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
No |
number, integer or string |
No |
- |
- |
8.1. Property WfExS-backend stage definition > placeholders > additionalProperties
#
Type |
|
Required |
No |
9. Property WfExS-backend stage definition > params
#
Type |
|
Required |
No |
Additional properties |
|
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 |
|
Required |
No |
Additional properties |
|
Defined in |
#/definitions/Param |
9.1.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 0
#
Type |
|
Required |
No |
9.1.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1
#
Type |
|
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 |
---|---|
- |
9.1.2.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 1 > item 1 items#
Type |
|
Required |
No |
9.1.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2
#
Type |
|
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 |
---|---|
- |
9.1.3.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 2 > item 2 items#
Type |
|
Required |
No |
9.1.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3
#
Type |
|
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 |
---|---|
- |
9.1.4.1. WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 3 > item 3 items#
Type |
|
Required |
No |
9.1.5. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > DirFile
#
Type |
|
Required |
No |
Additional properties |
|
Defined in |
#/definitions/DirFile |
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
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 |
No |
object |
No |
Same as url |
Secondary URLs / URIs are pointing to contents which will feed secondary inputs (CWL concept) |
|
No |
boolean or string |
No |
- |
Preferred base name / relative path for this input, instead of the derived one from the URL |
|
No |
boolean or string |
No |
- |
Put contents fetched for this input in this relative directory. This option does not affect preferred-name |
|
No |
string |
No |
- |
Use an explicitly named security context |
|
No |
boolean |
No |
- |
Whether this input contents can be included in RO-Crates or exported |
|
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 |
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 |
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 |
|
Required |
No |
Additional properties |
9.1.5.1.1. If (c-l-a-s-s = Must be one of:#
“Directory”
“File” )
Type |
|
Required |
No |
Additional properties |
9.1.5.1.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.2.1. If (c-l-a-s-s = “ContentWithURIs” )#
Type |
|
Required |
No |
Additional properties |
9.1.5.2.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.3.1. If (c-l-a-s-s = Must be one of:#
“Directory”
“File” )
Type |
|
Required |
No |
Additional properties |
9.1.5.3.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.4.1. If (c-l-a-s-s = “Directory” )#
Type |
|
Required |
No |
Additional properties |
9.1.5.4.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.5.1. If (c-l-a-s-s = “File” )#
Type |
|
Required |
No |
Additional properties |
9.1.5.5.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.6.1. If (c-l-a-s-s = “ContentWithURIs” )#
Type |
|
Required |
No |
Additional properties |
9.1.5.6.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.7.1. If (c-l-a-s-s = “Value” )#
Type |
|
Required |
No |
Additional properties |
9.1.5.7.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
9.1.5.8.1. If (c-l-a-s-s = “ContentWithURIs” )#
Type |
|
Required |
No |
Additional properties |
9.1.5.8.1.1. Must not be#
Type |
|
Required |
No |
Additional properties |
9.1.5.8.1.1.1. The following properties are required#
globExplode
autoFill
autoPrefix
If(_complex condition_)
Type |
|
Required |
No |
Additional properties |
9.1.5.8.1.1.2. Must not be#
Type |
|
Required |
No |
Additional properties |
9.1.5.8.1.1.2.1. The following properties are required#
value
IfNot(_complex condition_)
Type |
|
Required |
No |
Additional properties |
9.1.5.8.1.1.3. Must not be#
Type |
|
Required |
No |
Additional properties |
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 |
|
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 |
|
Required |
No |
Additional properties |
Description: When ‘c-l-a-s-s’ is a single file or a value, the assigned value
9.1.5.10.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > value > oneOf > item 0
#
Type |
|
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 |
|
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 |
---|---|
- |
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 |
|
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 |
|
Required |
No |
Additional properties |
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 |
---|---|---|---|---|---|
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 |
No |
string |
No |
- |
The regular expression used to split the tabulated content by columns |
|
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 |
|
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 |
---|---|
- |
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 |
|
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 |
|
Required |
No |
Default |
|
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 |
|
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 |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Additional properties |
|
Defined in |
#/definitions/InputURI |
Description: The URL(s) / URI(s) where this input is available
One of(Option) |
---|
9.1.5.12.1. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlainURI
#
Type |
|
Required |
No |
Same definition as |
9.1.5.12.2. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > PlaceholderURI
#
Type |
|
Required |
No |
Defined in |
#/definitions/PlaceholderURI |
Restrictions |
|
---|---|
Min length |
1 |
Must match regular expression |
|
9.1.5.12.3. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > LicensedURI
#
Type |
|
Required |
No |
Additional properties |
|
Defined in |
#/definitions/LicensedURI |
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 |
|
Required |
Yes |
Additional properties |
Description: The URI of the resource
Any of(Option) |
---|
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 |
|
Required |
No |
Same definition as |
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 |
|
Required |
No |
Same definition as |
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 |
|
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 |
---|---|
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 |
|
Required |
No |
Default |
|
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 |
|
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 |
---|---|
- |
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 |
|
Required |
No |
Additional properties |
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 |
|
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 |
|
Required |
Yes |
Same definition as |
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 |
|
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 |
---|---|
- |
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 |
|
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 |
|
Required |
No |
Restrictions |
|
---|---|
Min length |
1 |
Must match regular expression |
|
9.1.5.12.4. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > url > oneOf > item 3
#
Type |
|
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 |
---|---|
- |
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 |
|
Required |
No |
Additional properties |
One of(Option) |
---|
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 |
|
Required |
No |
Additional properties |
|
Same definition as |
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 |
|
Required |
No |
Same definition as |
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 |
|
Required |
No |
Same definition as |
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 |
|
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 |
---|---|
- |
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 |
|
Required |
No |
Additional properties |
One of(Option) |
---|
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 |
|
Required |
No |
Additional properties |
|
Same definition as |
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 |
|
Required |
No |
Same definition as |
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 |
|
Required |
No |
Same definition as |
9.1.5.13. Property WfExS-backend stage definition > params > ^(?!c-l-a-s-s)[^:;]+$ > oneOf > item 4 > secondary-urls
#
Type |
|
Required |
No |
Additional properties |
|
Same definition as |
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 |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Default |
|
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 |
|
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 |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Default |
|
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 |
|
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 |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Default |
|
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 |
|
Required |
No |
Additional properties |
|
Same definition as |
10. Property WfExS-backend stage definition > profile
#
Type |
|
Required |
No |
Additional properties |
Description: For engines which support profiles, like Nextflow or snakemake, if defined, the profile/s to enable
10.1. Property WfExS-backend stage definition > profile > oneOf > item 0
#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Min length |
1 |
Must match regular expression |
|
10.2. Property WfExS-backend stage definition > profile > oneOf > item 1
#
Type |
|
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 |
---|---|
- |
10.2.1. WfExS-backend stage definition > profile > oneOf > item 1 > item 1 items#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Min length |
1 |
Must match regular expression |
|
11. Property WfExS-backend stage definition > environment
#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
|
Defined in |
#/definitions/EnvVar |
Description: The name of an environment variable. These names cannot contain either the equal or the character \0
11.1.1. Property WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > item 0
#
Type |
|
Required |
No |
11.1.2. Property WfExS-backend stage definition > environment > ^[^=\0]+$ > oneOf > DirFile
#
Type |
|
Required |
No |
Additional properties |
|
Same definition as |
12. Property WfExS-backend stage definition > outputs
#
Type |
|
Required |
No |
Additional properties |
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 |
|
Required |
No |
Additional properties |
Property |
Pattern |
Type |
Deprecated |
Definition |
Title/Description |
---|---|---|---|---|---|
No |
enum (of string) |
No |
- |
- |
|
No |
Combination |
No |
- |
Output cardinality |
|
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) |
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 |
|
Required |
Yes |
Must be one of:
“File”
“Directory”
12.1.2. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality
#
Title: Output cardinality
Type |
|
Required |
No |
Additional properties |
|
Default |
|
Description: Expected cardinality of this output
12.1.2.1. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 0
#
Type |
|
Required |
No |
Must be one of:
“1”
“?”
“*”
“+”
12.1.2.2. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 1
#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Minimum |
≥ 0 |
12.1.2.3. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2
#
Type |
|
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 |
---|---|
- |
|
- |
12.1.2.3.1. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 0#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Minimum |
≥ 0 |
12.1.2.3.2. WfExS-backend stage definition > outputs > ^[^:;]+$ > cardinality > oneOf > item 2 > item 2 item 1#
Type |
|
Required |
No |
Restrictions |
|
---|---|
Minimum |
≥ 1 |
12.1.3. Property WfExS-backend stage definition > outputs > ^[^:;]+$ > preferredName
#
Type |
|
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 |
|
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 |
|
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 |
|
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 |
|
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