Fastqc

Quality control tool for high throughput sequence data

Citation

Citation: 10.1093/bioinformatics/btp641

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - fastqc

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

run

Run FastQC on one or more FASTQ files

Basic Usage:

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

Examples

Run Example

library(ShennongTools)

result <- sn_run("fastqc", "run",
  reads = "input_file.txt",
  output_dir = "output_file.txt",
  threads = 4,
  format = ""
)

# 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
`reads`	fastq	Yes	Input FASTQ files (single-end or paired-end)

Outputs:

Parameter	Type	Required	Description
`output_dir`	directory	Yes	Output directory containing FastQC reports

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads to use
`extract`	boolean	TRUE	Whether to extract the output zip files
`format`	string	“”	Optional input format override (e.g., bam)
`extras`	string	“”	Additional arguments to pass to FastQC