nf-core/sickle @ 0.0.0-3fc6d40
Summary
A windowed adaptive trimming tool for FASTQ files using quality
Get started
Add the following snippet to your workflow script to include this module.
include { SICKLE } from 'nf-core/sickle'
License
MIT License
Name
|
SICKLE |
|---|
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
|
log
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false, qual:'Illumina' ] |
|---|---|
*.log
file
|
log file *.log
|
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
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
|
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
|
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:31:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsickle/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sickle/blobs/sha256:8f1423006b7ac778bf77223157cd8f024aac1666fdcd6aeae427b9fb246d3f11 |
| Size | 2.8 KB |
| Checksum | sha256:8f1423006b7ac778bf77223157cd8f024aac1666fdcd6aeae427b9fb246d3f11 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:46:09 (UTC) | 1 | 2.8 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:31:49 (UTC) | 1 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:37:55 (UTC) | 1 | 2.8 KB |