Adapter and quality trimming of sequencing reads
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
contaminants{:bash}
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
*.fastq.gz{:bash}
The trimmed/modified fastq reads
*fastq.gz
log{:bash}
*.log{:bash}
Bbduk log file
*bbduk.log
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
BBMap is a short read aligner, as well as various other bioinformatic tools.
