Store and find Nextflow weblog payloads.

Check out:

• Run flowstore - How to quickly run flowstore
• Development - How to continue developing flowstore
• Configure databases - How to link to a running database instance
• Endpoints - API endpoints
• Underlying Data Models

flowstore is bundled as an executable jar, so you can just start the application with:

java -jar nfxlogger-<version>.jar

Keep in mind that this will run the flowstore with the default configuration setup.

You can pass your own configuration file with:

java -Dmicronaut.config.files=myconfig.yml -jar nfxlogger-<version>.jar

The default port bound is 8080. If you want to change that, you can pass the micronaut property like this:

java -Dmicronaut.server.port=8081 -jar nxflogger-<version>.jar

flowstore's dependencies are managed with Maven. Clone the code from GitHub and checkout the development branch:

git clone [email protected]:qbicsoftware/nextflow-logger-service.git
git checkout --track origin/development

Be sure you have Maven installed on your system and that the application is in your system PATH, otherwise the following commands will not work.

Open your terminal and verify the Maven installation. This will look different on your system, but should output the installed Maven version:

> mvn --version
Apache Maven 3.6.0 (97c98ec64a1fdfee7767ce5ffb20918da4f719f3; 2018-10-24T20:41:47+02:00)
Maven home: /usr/local/Cellar/maven/3.6.0/libexec
Java version: 1.8.0_181, vendor: Azul Systems, Inc., runtime: /Users/sven1103/.sdkman/candidates/java/8.0.181-zulu/jre
Default locale: en_GB, platform encoding: UTF-8
OS name: "mac os x", version: "10.14.5", arch: "x86_64", family: "mac"

mvn clean compile

mvn clean test

mvn clean verify

This will create an executable jar in your current working directory under ./target.

mvn clean package

Flowstore comes with a default configuration and variable placeholders that can be defined by the system environment.

micronaut:
    application:
        name: nxflogger
    router:
        static-resources:
            swagger:
                paths: classpath:META-INF/swagger
                mapping: /swagger/**
contact:
    first-name: ${wf-contact-first-name:Max}
    last-name: ${wf-contact-last-name:Mustermann}
    email: ${wf-contact-email:'[email protected]'}
database:
    name: workflows
datasources:
        default:
            url: jdbc:mariadb://${wf-db-host}/${wf-db-name}?maxPoolSize=150&pool
            username: ${wf-db-user}
            password: ${wf-db-pwd}
            driverClassName: org.mariadb.jdbc.Driver
endpoints:
    health:
        enabled: true
        sensitive: false
        details-visible: ANONYMOUS

This basic configuration can be used, if you have a MariaDB instance as data source. The default WeblogStorage interface implementation is for MariaDB, so if you want to use a different backend database, you need to change the driver and provide an own implementation of this interface.

Returns a JSON with a list of all stored workflow basic run information.

Expects a JSON weblog payload from Nextflow and stores it.

Returns basic workflow run information for workflow with a given run id.

Returns detailed Nextflow trace information for a workflow with a given run id.

Returns detailed workflow metadata such as parameter settings, input files and manifest information.

Coming soon...

This software is created by sven1103, developed at the Quantitative Biology Center, University of Tübingen, Germany.