Fastp

Fast all-in-one preprocessing for FastQ files

Citation

Citation: 10.1093/bioinformatics/bty560

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - fastp

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

trim

Trim and filter reads in FASTQ files

Basic Usage:

result <- sn_run("fastp", "trim",
  # Add your parameters here
)

Examples

Trim Example

library(ShennongTools)

result <- sn_run("fastp", "trim",
  input1 = "sample_R1.fastq.gz",
  output1 = "output_file.txt",
  threads = 4
)

# 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

trim Parameters

Inputs:

Parameter	Type	Required	Description
`input1`	fastq	Yes	First input FASTQ file (R1)
`input2`	fastq	No	Second input FASTQ file (R2, optional)

Outputs:

Parameter	Type	Required	Description
`output1`	fastq	Yes	First output FASTQ file (R1)
`output2`	fastq	No	Second output FASTQ file (R2)
`html_report`	html	No	HTML quality control report
`json_report`	json	No	JSON quality control report

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads to use
`extras`	string	“”	Additional arguments to pass to fastp