Nextflow Registry | nf-core/fastp@0.0.0-6c4ed3a

nf-core/fastp @ 0.0.0-6c4ed3a

Perform adapter/quality trimming on sequencing reads

trimming quality control fastq

Latest version: 0.0.0-6c4ed3a

Total downloads: 2

Source: nf-core/modules

Authors: @drpatelh @kevinmenden @eit-maxlcummins

Maintainers: @drpatelh @kevinmenden

Perform adapter/quality trimming on sequencing reads

Add the following snippet to your workflow script to include this module.

include { FASTP } from 'nf-core/fastp'

MIT License

Process

`Name`	`FASTP`

Input 4 channels

#1 tuple

`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.
`adapter_fasta` file	File in FASTA format containing possible adapters to remove. `*.{fasta,fna,fas,fa}`

`discard_trimmed_pass` boolean	Specify true to not write any reads that pass trimming thresholds. This can be used to use fastp for the output report only.

`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 a file ending in `*.merged.fastq.gz`

Output 7 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	fastq log file `*.log`

#2 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.html` file	Results in HTML format `*.html`

#3 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.json` file	Results in JSON format `*.json`

#4 reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fastp.fastq.gz` file	The trimmed/modified/unmerged fastq reads `*fastp.fastq.gz`

#5 reads_fail tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fail.fastq.gz` file	Reads the failed the preprocessing `*fail.fastq.gz`

#6 reads_merged tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.merged.fastq.gz` file	Reads that were successfully merged `*.{merged.fastq.gz}`

#7 versions_fastp tuple

`${task.process}` string	The name of the process
`fastp` string	The name of the tool
`fastp --version 2>&1 \| sed -e "s/fastp //g"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
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.	n/a

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:16:48 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ffastp/0.0.0-6c4ed3a/download