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

trim_log (file)

trimmomatic log file, from the trim_log parameter

*.log

out_log (file)

log of output from the standard out

*.log

summary (file)

trimmomatic summary file of surviving and dropped reads

*.summary

versions (file)

File containing software versions

versions.yml