Multiqc

Aggregate results from bioinformatics analyses into a single report

Citation

Citation: 10.1093/bioinformatics/btw354

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - multiqc

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("multiqc", "run", ...)

Available Commands

run

Run MultiQC on the specified input directory to generate a summary report

Basic Usage:

result <- sn_run("multiqc", "run",
  # Add your parameters here
)

Examples

Run Example

library(ShennongTools)

result <- sn_run("multiqc", "run",
  input_dir = "input_file.txt"
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Parameters Reference

run Parameters

Inputs:

Parameter	Type	Required	Description
`input_dir`	directory	Yes	Directory containing result files (e.g., from FastQC, STAR, etc.)

Outputs:

Parameter	Type	Required	Description
`output_dir`	directory	No	Output directory for the MultiQC report

Parameters:

Parameter	Type	Default	Description
`output_name`	string	“multiqc_report.html”	Custom name for the output HTML report
`force`	boolean	TRUE	Overwrite output directory if it exists
`modules`	string	“”	Comma-separated list of specific modules to run (optional)
`extras`	string	“”	Additional command-line arguments to pass to MultiQC