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