Realign reads mapped with BWA to elongated reference genome
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
bam
:file
BAM/SAM file
*.{bam,sam}
meta2
:map
Groovy Map containing reference information
e.g. [ id:'test' ]
fasta
:file
Input elongated genome fasta
meta3
:map
Groovy Map containing reference information
e.g. [ id:'test' ]
elongation_factor
:integer
The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by
meta4
:map
Groovy Map containing reference information
e.g. [ id:'test' ]
elongated_chr_list
:file
File listing the chromosomes that were elongated
*_elongated
Output
name:type
description
pattern
bam
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*_realigned.bam
:file
Realigned BAM file
*.bam
versions_circularmapper
${task.process}
:string
The process the versions were collected from
circularmapper
:string
The tool name
1.93.5
:string
The command used to generate the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The process the versions were collected from
circularmapper
:string
The tool name
1.93.5
:string
The command used to generate the version of the tool
Tools
circularmapper
GPL v3
A method to improve mappings on circular genomes such as Mitochondria.
