Adapter and quality trimming of short-read FASTQ data using chelae.
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information. Use ‘single_end: true’ to specify
single-end FASTQs, or ‘single_end: false’ for paired-end reads.
e.g. [ id:‘test’, single_end:false ]
reads
:file
List of input FastQ files. One file for single-end data, two files for
paired-end data (R1 and R2).
*.{fastq,fastq.gz,fq,fq.gz}
adapter_fasta
:file
Optional FASTA file of adapter sequences. The best-matching adapter will
be trimmed. Use an empty list [] when not supplying an adapter file;
adapter kits can be specified via ext.args using –kit instead.
*.{fasta,fna,fas,fa}
Output
name:type
description
pattern
reads
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.chelae.fastq.gz
:file
Trimmed FASTQ file(s), BGZF-compressed. Single file for SE; R1 and R2
files for PE.
*.chelae.fastq.gz
json
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.chelae.json
:file
fastp-compatible JSON trimming report, consumable by MultiQC.
*.chelae.json
metrics
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.chelae.tsv
:file
Tab-separated trimming metrics summary.
*.chelae.tsv
versions_chelae
${task.process}
:string
The name of the process
chelae
:string
The name of the tool
chelae --version 2>&1 | sed 's/chelae //'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
chelae
:string
The name of the tool
chelae --version 2>&1 | sed 's/chelae //'
:eval
The expression to obtain the version of the tool
Tools
chelae
MIT
A fast, accurate, multi-threaded toolkit for trimming and filtering short-read
FASTQ data, written in Rust. Outputs BGZF-compressed FASTQ and a fastp-compatible
JSON report suitable for MultiQC.
