Performs quality and adapter trimming on paired end and single end reads
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads:file
Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.
*.fastq.gz
trimmed_reads
*.paired.trim*.fastq.gz:file
The trimmed/modified paired end fastq reads
*.paired.trim*.fastq.gz
unpaired_reads
*.unpaired.trim_*.fastq.gz:file
The trimmed/modified unpaired end fastq reads
*.unpaired.trim_*.fastq.gz
trim_log
*_trim.log:file
trimmomatic log file, from the trim_log parameter
*.log
out_log
*_out.log:file
log of output from the standard out
summary
*.summary:file
trimmomatic summary file of surviving and dropped reads
*.summary
versions
versions.yml:file
File containing software versions
versions.yml
A flexible read trimming tool for Illumina NGS data
