RepeatFS

RepeatFS records file and I/O provenance at the file-system level to enable replication and verification of bioinformatics computational workflows.

Key Features:

• Provenance Recording: Records file and I/O operations and stores provenance metadata required to trace and reproduce analyses.
• Workflow Replication and Verification: Verifies software versions, command-line parameters, and other execution attributes against original runs and reports deviations.
• FUSE-based Filesystem Operation: Implements a FUSE (Filesystem in Userspace) filesystem to capture I/O for Linux command-line software at the file-system layer.
• Provenance Visualization and Task Automation: Provides provenance visualization and task automation capabilities to aid interpretation of workflow history and automate repetitive processes.

Scientific Applications:

• Bioinformatics Workflow Replication: Replicates bioinformatics analyses involving large numbers of operations (reported over one million operations) without altering original methods.
• Identification of Software-induced Variability: Identifies software inconsistencies that lead to replication differences by comparing versions and parameters.
• Cross-environment Reproducibility Verification: Enables verification of analysis integrity across different computational environments (Linux-based).

Methodology:

Implemented in Python 3 as a FUSE (Filesystem in Userspace) module, RepeatFS captures file and I/O operations, records provenance metadata, verifies software versions and command-line parameters, reports deviations, and provides provenance visualization and task automation.