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Configuration

Local WfExS Configuration​

The local configuration for WfExS is provided in a YAML (.yaml/.yml) file. An initial local configuration can be made by running the following command in an empty directory:

./WfExS_backend.py init

An example local config may look like:

workDir: ./wfexs-backend-test_WorkDir
cacheDir: ./wfexs-backend-test
crypt4gh:
  key: local_config.yaml.key
  passphrase: strive backyard dividing gumball
  pub: local_config.yaml.pub
tools:
  dockerCommand: docker
  containerType: singularity
  encrypted_fs:
    type: encfs
    command: encfs
  engineMode: local
  gitCommand: git
  javaCommand: java
  singularityCommand: singularity
  staticBashCommand: bash-linux-x86_64

Under tools, specify the commands to run programs like singularity, java, docker, etc. If only the names are specified, as above, these programs must be in $PATH. If any are not in $PATH, either add them to $PATH or give the full path to the progam here.

Workflow Configuration​

The workflow configuration is also given in a YAML file. Template:

workflow_id: # URL to workflow
workflow_config:
  secure: false
cacheDir: /path/to/chacheDir
crypt4gh:
  key: /path/to/private-key
  passphrase: four random words here
  pub: /path/to/public-key
params:
  ...
outputs:
  ...

The params are the inputs to your workflow. The outputs map to the expected files/directories that come out at the end of the workflow.

More information can be found at https://github.com/inab/WfExS-backend#configuration-files.