Merging overlapping paired reads into a single read.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
reads{:bash}
:file
List of input paired end fastq files
*.{fastq,fq}.gz
interleave{:bash}
:boolean
Indicates whether the input paired reads are interleaved or not
merged{:bash}
*_merged.fastq.gz{:bash}
merged reads
*_merged.fastq
unmerged{:bash}
*_unmerged.fastq.gz{:bash}
unmerged reads
*_unmerged.fastq
ihist{:bash}
*_ihist.txt{:bash}
insert size histogram
*_ihist.txt
log{:bash}
*.log{:bash}
log file containing stdout and stderr from bbmerge.sh
*.log
versions_bbmap{:bash}
${task.process}{:bash}
:string
The name of the process
bbmap{:bash}
The name of the tool
bbversion.sh | grep -v "Duplicate cpuset"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
BBMap is a short read aligner, as well as various other bioinformatic tools.
