Adapter and quality trimming of sequencing reads
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
contaminants
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
*.fastq.gz
The trimmed/modified fastq reads
*fastq.gz
log
*.log
Bbduk log file
*bbduk.log
versions_bbmap
${task.process}
:string
The name of the process
bbmap
The name of the tool
bbversion.sh | grep -v "Duplicate cpuset"
:eval
The expression to obtain the version of the tool
versions
BBMap is a short read aligner, as well as various other bioinformatic tools.
