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

nf-core/sickle @ 0.0.0-0c7146d

A windowed adaptive trimming tool for FASTQ files using quality

fastq sliding window trimming

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @BioInf2305

Maintainers: @BioInf2305

A windowed adaptive trimming tool for FASTQ files using quality

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

include { SICKLE } from 'nf-core/sickle'

MIT License

Process

`Name`	`SICKLE`

Input 1 channel

#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. File of forward reads must be supplied first and reverse reads as the second e.g. ["read.1.fastq.gz","read.2.fastq.gz"] `*.{fq,fastq,fq.gz,fastq.gz}`
`qual_type` string	sickle needs a base quality values, which could be either illumina, solexa or sanger `illumina or solexa or sanger`

Output 5 channels

#1 log tuple

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

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 paired_trimmed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false, qual:'Illumina' ]
`${prefix}.pe{1,2}.trimmed.fastq.gz` file	5' or 3' trimmed (based on base quality) paired-end fastq files `*.pe{1,2}.trimmed.fastq.gz`

#4 single_trimmed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false, qual:'Illumina' ]
`${prefix}.se.trimmed.fastq.gz` file	5' or 3' trimmed (based on base quality) single-end fastq file `*.se.trimmed.fastq.gz`

#5 singleton_trimmed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false, qual:'Illumina' ]
`${prefix}.singleton.trimmed.fastq.gz` file	5' or 3' trimmed (based on base quality) singleton fastq file `*.singleton.trimmed.fastq.gz`

Tool	Description	Homepage
sickle	a tool that determines clipping of reads on 3' end and 5'end based on base quality	https://github.com/najoshi/sickle

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:14:04 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsickle/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sickle/blobs/sha256:183ad572b413f89c815643fadf0411c12a9a7dc7df9c494f8a17bee37f49d217
Size	2.8 KB
Checksum	sha256:183ad572b413f89c815643fadf0411c12a9a7dc7df9c494f8a17bee37f49d217
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:14:04 (UTC)		1	2.8 KB	-