Nextflow Registry | nf-core/adapterremoval@0.0.0-0c7146d

nf-core/adapterremoval @ 0.0.0-0c7146d

Trim sequencing adapters and collapse overlapping reads

trimming adapters merging fastq

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @maxibor @jfy133

Maintainers: @maxibor @jfy133

Trim sequencing adapters and collapse overlapping reads

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

include { ADAPTERREMOVAL } from 'nf-core/adapterremoval'

MIT License

Process

`Name`	`ADAPTERREMOVAL`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information 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. `*.{fq,fastq,fq.gz,fastq.gz}`

`adapterlist` file	Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args.

Output 8 channels

#1 settings tuple

`meta` map	Groovy Map containing sample information
`*.settings` file	AdapterRemoval log file `*.settings`

#2 collapsed tuple

`meta` map	Groovy Map containing sample information
`${prefix}.collapsed.fastq.gz` file	Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair but were not trimmed. `*.collapsed.fastq.gz`

#3 discarded tuple

`meta` map	Groovy Map containing sample information
`${prefix}.discarded.fastq.gz` file	Adapter trimmed FastQ files of reads that did not pass filtering thresholds. `*.discarded.fastq.gz`

#4 paired_truncated tuple

`meta` map	Groovy Map containing sample information
`${prefix}.pair{1,2}.truncated.fastq.gz` file	Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge with their respective R{1,2} pair due to long templates. The respective pair is stored in 'pair{1,2}_truncated'. `*.pair{1,2}.truncated.fastq.gz`

#5 singles_truncated tuple

`meta` map	Groovy Map containing sample information
`${prefix}.truncated.fastq.gz` file	Adapter trimmed FastQ files of either single-end reads, or singleton 'orphaned' reads from merging of paired-end data (i.e., one of the pair was lost due to filtering thresholds). `*.truncated.fastq.gz`

#6 paired_interleaved tuple

`meta` map	Groovy Map containing sample information
`${prefix}.paired.fastq.gz` file	Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads `*.paired.fastq.gz`

#7 collapsed_truncated tuple

`meta` map	Groovy Map containing sample information
`${prefix}.collapsed.truncated.fastq.gz` file	Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair and were trimmed of adapter due to sufficient overlap. `*.collapsed.truncated.fastq.gz`

#8 versions_adapterremoval tuple

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

Tool	Description	Homepage
adapterremoval	The AdapterRemoval v2 tool for merging and clipping reads.	https://github.com/MikkelSchubert/adapterremoval

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:20:59 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules