WfExS-backend configuration file (EOSC-Life Demonstrator 7 JSON Schemas)
No Additional Properties @@ -47,7 +47,7 @@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.
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
+ crypt4ghWfExS-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 @@ -120,7 +120,7 @@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
@@ -161,7 +161,7 @@Passphrase which has to be used to work with the secret key
@@ -202,7 +202,7 @@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
@@ -240,7 +240,7 @@External tools configuration block
No Additional Properties @@ -277,8 +277,8 @@Type of container technology to be used when any workflow is launched using this installation. Supported types are:
+ containerType
Type of container technology to be used by default when any workflow is launched using this installation. Supported types are:
- Singularity (default).
- Docker.
- Podman
@@ -326,7 +326,7 @@
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.
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
When this key is set, it overrides the default command to be used when an encrypted directory has to be created or mounted
@@ -512,8 +512,8 @@Path to unmounting command to be used, being 'fusermount' by default
+ fusermount_commandPath to unmounting command to be used, being 'fusermount' by default
@@ -560,7 +560,7 @@Number of minutes before an idle, mounted encrypted directory will automatically unmount
@@ -577,6 +577,192 @@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 ItemsInternal symbolic name used to represent this command
+ + + + + + + +Either the absolute path or PATH findable program name
+ + + + +Must be at least 1 characters long
Git is used to materialize workflows being hosted at git repositories, like GitHub. This key sets up custom paths to git command
@@ -646,7 +832,7 @@Java is needed to run Nextflow and future workflow engines. This key sets up custom paths to java installations
@@ -687,8 +873,8 @@Singularity is used when containerType is 'singularity'. This key sets up custom paths to singularity command
+ singularityCommandSingularity is used when containerType is 'singularity'. This key sets up custom paths to singularity command
@@ -728,8 +914,8 @@Docker is used when containerType is 'docker'. This key sets up custom paths to docker command
+ dockerCommandDocker is used when containerType is 'docker'. This key sets up custom paths to docker command
@@ -769,8 +955,8 @@Podman is used when containerType is 'podman'. This key sets up custom paths to podman command
+ podmanCommandPodman is used when containerType is 'podman'. This key sets up custom paths to podman command
@@ -810,8 +996,8 @@'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
+ dotCommand'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
@@ -851,8 +1037,8 @@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.
+ staticBashCommandThere 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.
@@ -892,8 +1078,8 @@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.
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.
(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
(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
Version of Nextflow engine to be used when workflow's metadata does not provide hints about minimal version needed.
+ versionVersion of Nextflow engine to be used when workflow's metadata does not provide hints about minimal version needed.
@@ -1072,7 +1258,7 @@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
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
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
@@ -1367,7 +1553,7 @@This is a wildcard declaration to allow setting up custom paths to commands needed by several parts of the code
@@ -1405,7 +1591,7 @@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).
Some fetchers could need customizations at the configuration level, like limiting throughput or setting up some proxy
@@ -1482,7 +1668,7 @@Some scheme fetchers could need customizations which depend on local WfExS installation environment. This is the place where to pass that
@@ -1501,6 +1687,6 @@