qbic-nextflow-api

A RESTful API, which enables access to cluster jobs, submitted with Nextflow.

API planning

• Make a list of information, that should be accessible over the API
• Design a basic API specification with swagger
• Create Java Spring stub classes from swagger
• Implement API with Java Spring Boot
• Implement database for storing the meta information of a Nextflow workflow
• Implement information transfer in an example Nextflow script, with database INSERT commands

Brainstorming

Necessary information

General workflow information

This can be information, which is actually interesting for doing workflow statistics. For example get workflows of a certain type, from a certain userID, workflows that failed, workflows that succeeded and so on.

Workflow specific information

Specific information can be captured by the Nextflow's introspection features:

• scriptId
• scriptName
• scriptFile
• repository
• commitId
• revision
• projectDir
• launchDir
• workDir
• configFiles
• container
• commandLine
• profile
• runName
• sessionId
• resume
• start

Accessible in the workflow completion handler only:

• complete
• duration

Accessible in the workflow completion and error handlers only:

• success
• exitStatus
• errorMessage
• errorReport

An additional information would be a userId, which is a meta information that can come from a third party software, such as a portal runtime environment.

This information can be provided in a metadata.yaml file, which gets parsed in the beginning of the pipeline execution and grabs user information.