track_external_tools: Track External Bioinformatics Tools

In Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

Track External Bioinformatics Tools

Description

Track versions of external command-line tools commonly used in bioinformatics pipelines (e.g., samtools, STAR, BWA, etc.)

Usage

track_external_tools(tools = NULL, registry_file)

Arguments

tools	Character vector of tool names to track. If NULL, tracks common tools.
registry_file	Character. Path to tools registry. Default ".capsule/tools_registry.json"

Value

List containing tool version information

Examples

## Not run: 
# Track common bioinformatics tools
track_external_tools(registry_file = tempfile(fileext = ".json"))

# Track specific tools
track_external_tools(c("samtools", "bwa", "STAR"),
                     registry_file = tempfile(fileext = ".json"))

## End(Not run)

Capsule documentation built on Nov. 11, 2025, 5:14 p.m.