Bpipe

Bpipe automates definition and execution of computational pipelines to enable reproducible and maintainable bioinformatics analyses.

Key Features:

• Dedicated programming language: Provides a dedicated programming language for defining pipelines and pipeline stages.
• Shell and CLI integration: Transforms existing shell script–based and command-line tool workflows into structured pipeline stages.
• Controlled execution: Executes pipelines with controlled job management to support reliable runs.
• Reproducibility and audit trails: Records comprehensive logs and audit trails for verification and replication of analyses.
• Automation of repetitive tasks: Manages and automates repetitive bioinformatics analysis tasks within pipelines.
• Java runtime dependency: Requires the Java runtime as its dependency for execution.

Scientific Applications:

• Reproducible computational analyses: Enables replication and validation of computational biology analyses through logged, auditable pipeline runs.
• Workflow conversion and maintenance: Converts shell script–based and command-line tool workflows into maintainable, versionable pipelines for bioinformatics processing.

Methodology:

Pipeline definitions are written in Bpipe's dedicated programming language, which executes shell commands and command-line tools as pipeline stages while generating logs and audit trails; the system runs on the Java runtime.