Split sequencing reads by mapping them to multiple references simultaneously
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.
index{:bash}
:directory
Directory to place generated index
*
primary_ref{:bash}
Path to the primary reference
other_ref_names{:bash}
:list
List of other reference ids apart from the primary
other_ref_paths{:bash}
Path to other references paths corresponding to “other_ref_names”
only_build_index{:bash}
:string
true = only build index; false = mapping
bbsplit_index{:bash}
Directory with index files
bbsplit_index
primary_fastq{:bash}
*primary*fastq.gz{:bash}
Output reads that map to the primary reference
*primary*fastq.gz
all_fastq{:bash}
*fastq.gz{:bash}
All reads mapping to any of the references
*fastq.gz
stats{:bash}
*txt{:bash}
Tab-delimited text file containing mapping statistics
*.txt
log{:bash}
*.log{:bash}
Log file
*.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.
