.calculate_checksum

Internal function to calculate file checksum using appropriate algorithm
based on file size. Large files use faster xxHash, small files use SHA-256.

internal

A comprehensive reproducibility framework designed for R and bioinformatics
workflows. Automatically captures the entire analysis environment including R session
info, package versions, external tool versions ('Samtools', 'STAR', 'BWA', etc.), 'conda'
environments, reference genomes, data provenance with smart checksumming for large files,
parameter choices, random seeds, and hardware specifications. Generates executable scripts
with 'Docker', 'Singularity', and 'renv' configurations. Integrates with workflow managers
('Nextflow', 'Snakemake', 'WDL', 'CWL') to ensure complete reproducibility of computational
research workflows.

Abu SAADAT

Capsule

Comprehensive Reproducibility Framework for R and Bioinformatics
Analysis

.calculate_checksum function

<dl><dt>file_path</dt>
<dd>Character. Path to file</dd>
<dt>fast_hash</dt>
<dd>Logical. Whether to use fast hashing for large files</dd>
<dt>size_threshold_gb</dt>
<dd>Numeric. Size threshold in GB</dd>
<dt>file_size_gb</dt>
<dd>Numeric. Actual file size in GB</dd></dl>

Arguments

Calculate Checksum with Smart Algorithm Selection — .calculate_checksum

<dl>

<dt>file_path</dt>
<dd>Character. Path to file</dd>


<dt>fast_hash</dt>
<dd>Logical. Whether to use fast hashing for large files</dd>


<dt>size_threshold_gb</dt>
<dd>Numeric. Size threshold in GB</dd>


<dt>file_size_gb</dt>
<dd>Numeric. Actual file size in GB</dd>

</dl>

.calculate_checksum: Calculate Checksum with Smart Algorithm Selection

Description

Usage

Value

Arguments