fastp

Description¶

Perform adapter/quality trimming on sequencing reads

Keywords: trimming, quality control, fastq

Installation¶

ebi-metagenomics/fastp

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install fastp

Tools¶

fastp¶

A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

Input¶

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. e.g. [ id:'test', single_end:false ]	-
`reads`	file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. If you wish to run interleaved paired-end data, supply as single-end data but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.	-
`save_trimmed_fail`	boolean	Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`	-
`save_merged`	boolean	Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`	-

Output¶

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	-
`reads`	file	The trimmed/modified/unmerged fastq reads	`*fastp.fastq.gz`
`json`	file	Results in JSON format	`*.json`
`html`	file	Results in HTML format	`*.html`
`log`	file	fastq log file	`*.log`
`versions`	file	File containing software versions	`versions.yml`
`reads_fail`	file	Reads the failed the preprocessing	`*fail.fastq.gz`
`reads_merged`	file	Reads that were successfully merged	`*.{merged.fastq.gz}`