Filter out sequences by sequence header name(s)
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.
names_to_filter{:bash}
:string
String containing names of reads to filter out of the fastq files.
output_format{:bash}
String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2
interleaved_output{:bash}
:boolean
Whether to produce an interleaved fastq output file
*.${output_format}{:bash}
The trimmed/modified fastq reads
*${output_format}
log{:bash}
*.log{:bash}
filterbyname.sh log file
*.filterbyname.log
versions_bbmap{:bash}
${task.process}{:bash}
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.
