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CloWM Workflow Service

Description

This is the Workflow service of the CloWM service.

Environment Variables

Mandatory / Recommended Variables

Variable Default Value Description
PUBLIC_KEY_VALUE / PUBLIC_KEY_FILE randomly generated Public Key / Path to Public Key Public part of RSA Key in PEM format to verify JWTs
DB_HOST unset <db hostname / IP> IP or Hostname Address of DB
DB_PORT 3306 Number Port of the database
DB_USER unset <db username> Username of the database user
DB_PASSWORD unset <db password> Password of the database user
DB_DATABASE unset <db name> Name of the database
OBJECT_GATEWAY_URI unset HTTP URL HTTP URL of the Ceph Object Gateway
BUCKET_CEPH_ACCESS_KEY unset <access key> Ceph access key with admin privileges
BUCKET_CEPH_SECRET_KEY unset <secret key> Ceph secret key with admin privileges
OPA_URI unset HTTP URL HTTP URL of the OPA service
SLURM_ENDPOINT unset HTTP URL HTTP URL to communicate with the Slurm cluster
SLURM_TOKEN unset <JWT> JWT for communication with the Slurm REST API. Should belong to the user SLURM_USER

Optional Variables

Variable Default Value Description
API_PREFIX /api/workflow-service URL path Prefix before every URL path
BACKEND_CORS_ORIGINS [] json formatted list of urls List of valid CORS origins
SQLALCHEMY_VERBOSE_LOGGER False <"True"&#x7c;"False"> Enables verbose SQL output.
Should be false in production
PARAMS_BUCKET nxf-params Bucket Name Bucket where the nextflow configurations for each execution should be saved
WORKFLOW_BUCKET clowm-workflows Bucket Name Bucket where to save important workflow files
ICON_BUCKET clowm-icons Bucket name Bucket where to save workflow icons. Should be publicly available.
SLURM_USER slurm string User on the slurm cluster who should run the job. Should be the user of the SLURM_TOKEN
PARAMS_BUCKET_MOUNT_PATH /mnt/params-bucket Path on slurm cluster Folder where the S3 bucket PARAMS_BUCKET will be mounted on the slurm cluster
NX_CONFIG unset Path on slurm cluster Configuration file on the slurm cluster that is the same for every nextflow run
NX_BIN nextflow Path on slurm cluster Path to the nextflow executable. Default it is in the PATH
SLURM_WORKING_DIRECTORY /tmp Path on slurm cluster Working directory for the slurm job with the nextflow command
ACTIVE_WORKFLOW_EXECUTION_LIMIT 3 Integer Limit of active workflow execution a user is allowed to have. -1 means infinite.
DEV_SYSTEM False <"True"&#x7c;"False"> Activates an endpoint that allows execution of an workflow from an arbitrary Git Repository.
HAS TO BE False in PRODUCTION!
OPA_POLICY_PATH /clowm/authz/allow URL path Path to the OPA Policy for Authorization

Nextflow Variables

All Nextflow environment variables with the prefix NXF_ are also support when submitting a job to the slurm cluster, e.g. pinning the Nextflow version

NXF_VER=23.04.0