WfExS-backend config

Type: object

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

No Additional Properties

Caching directory

Type: string

Directory where all the cache-able content will be hold.
This directory can be removed, as its contents should be available outside.
When it is not set, a temporary directory is created for the session, being destroyed when the program finishes.

Must be at least 1 characters long

Installation Crypt4GH key setup

Type: object

WfExS-backend needs an encryption key for several tasks, like encrypting and decrypting random keys of encrypted working directories. When this block does not exist, WfExS-backend.py creates the installation's keys, and updates the configuration file

No Additional Properties

Secret key installation file

Type: string

The path to the Crypt4GH secret key file used by this installation. If the path is relative, the directory where the configuration file resides is used for the resolution

Must be at least 1 characters long

Passphrase used to work with the secret key

Type: string

Passphrase which has to be used to work with the secret key

Must be at least 0 characters long

Public key installation file

Type: string

The path to the Crypt4GH public key file used by this installation. If the path is relative, the directory where the configuration file resides is used for the resolution

Must be at least 1 characters long

External tools configuration block

Type: object

External tools configuration block

No Additional Properties

Default container technology type in this installation

Type: enum (of string) Default: "singularity"

Type of container technology to be used by default when any workflow is launched using this installation. Supported types are:
- Singularity (default).
- Docker.
- Podman
- No containerisation technology (discouraged)
Encrypted working directories are unsupported when Docker or Podman are used due technological limitations

Must be one of:

  • "singularity"
  • "docker"
  • "podman"
  • "none"

Workflow engine invocation mode

Type: enum (of string) Default: "local"

Most of workflow engines are usually available both as installable executables and as containers, but when they are used inside a container usually do not support running containerised jobs, unless a very careful setup is done. Currently, WfExS-backend only partially supports Nextflow in its docker-in-docker mode.

Must be one of:

  • "local"
  • "docker"

Working directory FUSE encrypted FS configuration block

Type: object
No Additional Properties

Type of encrypted FS

Type: enum (of string) Default: "gocryptfs"

When an encrypted working directory is needed, the type of encrypted FS to be used is set up through this key. Currently, both encfs (default) and gocryptfs (recommended) are supported

Must be one of:

  • "encfs"
  • "gocryptfs"

Path to encryption mount program

Type: string

When this key is set, it overrides the default command to be used when an encrypted directory has to be created or mounted

Path to unmount command

Type: string Default: "fusermount"

Path to unmounting command to be used, being 'fusermount' by default

Idle minutes before autoumount

Type: integer Default: 5

Number of minutes before an idle, mounted encrypted directory will automatically unmount

Custom command paths

Type: array of object

Different modules depend on locatable programs, like git, docker, java or similar. These declarations are used to provide WfExS either custom paths or custom names. These declarations take precedence over gitCommand, javaCommand and similar ones

Must contain a minimum of 1 items

All items must be unique

No Additional Items

Each item of this array must be:

Type: object

The command key

Type: string

Internal symbolic name used to represent this command

The command path

Type: string

Either the absolute path or PATH findable program name

Must be at least 1 characters long

Git client path

Type: string Default: "git"

Git is used to materialize workflows being hosted at git repositories, like GitHub. This key sets up custom paths to git command

Java path

Type: string Default: "java"

Java is needed to run Nextflow and future workflow engines. This key sets up custom paths to java installations

Singularity client path

Type: string Default: "singularity"

Singularity is used when containerType is 'singularity'. This key sets up custom paths to singularity command

Docker client path

Type: string Default: "docker"

Docker is used when containerType is 'docker'. This key sets up custom paths to docker command

Podman client path

Type: string Default: "podman"

Podman is used when containerType is 'podman'. This key sets up custom paths to podman command

'dot' client path

Type: string Default: "dot"

'dot' is used when the workflow engine generated diagram is in DOT format, to translate it to either PNG or SVG when the diagram is going to be embedded in an RO-Crate

Static bash command (used in singularity based Nextflow engine executions)

Type: string Default: "bash.static"

There is a bug in some bash versions which make them unsuitable to run the trace machinery from Nextflow, as the trace machinery enters in a live lock. As the images containing these faulty bash versions cannot be changed, a 'monkey patch' solution where an external, static bash version is injected on workflow execution is used. The injected static bash is found through this key, which is searched on PATH variable when it is not a full path.

Static ps command (used in Nextflow engine executions to assure metrics gathering works even in containers without /bin/ps command)

Type: string Default: "ps.static"

Nextflow uses a bash wrapper to gather process execution statistics. One of the binaries used by the wrapper is ps. Some containers (for instance, r-base:latest) do not contain such binary. As the images which do not contain ps cannot be changed, a 'monkey patch' solution where an external, static ps version is injected on workflow execution is used. The injected static ps is found through this key, which is searched on PATH variable when it is not a full path.

Type: object

Image for docker-in-docker mode

Type: string Default: "nextflow/nextflow"

(unfinished) When engineMode is docker, the name of the image to be fetched and used. The used tag will depend on the workflow's metadata, being by default the version

Nextflow's version

Type: string Default: "19.04.1"

Version of Nextflow engine to be used when workflow's metadata does not provide hints about minimal version needed.

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

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

Type: null

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]+.*$

Type: object

cwltool's version

Type: string Default: "3.1.20210628163208"

Version of cwltool engine to be used. WfExS is not currently guessing the minimal needed version, so it is either the value set up in this key or the default one

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: ^.+Command$

Path to a command

Type: string

This is a wildcard declaration to allow setting up custom paths to commands needed by several parts of the code

Must be at least 1 characters long

Working directory

Type: string

Directory where all the working directories are going to be created.
When it is not set, a temporary directory is created, which will be removed when the program finishes (which avoids inspecting the working directory after the program has finished).

Must be at least 1 characters long

Fetchers parameters setup

Type: object

Some fetchers could need customizations at the configuration level, like limiting throughput or setting up some proxy

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

Property name regular expression: ^[a-z][a-z0-9+.-]*$

Scheme fetcher setup

Type: object

Some scheme fetchers could need customizations which depend on local WfExS installation environment. This is the place where to pass that