Description

Performs quality and adapter trimming on paired end and single end reads

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.

*.fastq.gz

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

trimmed_reads (file)

The trimmed/modified paired end fastq reads

*.paired.trim*.fastq.gz

unpaired_reads (file)

The trimmed/modified unpaired end fastq reads

*.unpaired.trim_*.fastq.gz

log (file)

trimmomatic log file

*.log

summary (file)

trimmomatic summary file of surviving and dropped reads

*.summary

versions (file)

File containing software versions

versions.yml
included in
callingcards variantcatalogue viralintegration
author
Github user alyssa-ab
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Tools

trimmomatic
GPL v3

A flexible read trimming tool for Illumina NGS data

http://www.usadellab.org/cms/?page=trimmomatic github.com/usadellab/Trimmomatic 10.1093/bioinformatics/btu170