A method to improve mappings on circular genomes, using the BWA mapper.
meta
:map
Groovy Map containing reference information e.g. [ id:'sample1' ]
[ id:'sample1' ]
reference
:file
Genome fasta file
*.fasta
meta2
elongation_factor
:integer
The number of bases that the ends of the target chromosome in the reference genome should be elongated by
meta3
target
:string
The name of the chromosome in the reference genome that should be elongated
fasta
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*_${elongation_factor}.fasta
elongated
*${elongation_factor}_elongated
File listing the chromosomes that were elongated
*_elongated
versions_circulargenerator
${task.process}
The name of the process
circulargenerator
The name of the tool
circulargenerator -h | sed -n 's/usage: CircularGeneratorv//p'
:eval
The expression to obtain the version of the tool
versions
Creating a modified reference genome, with an elongation of the an specified amount of bases
