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