Polishing genome assemblies with short reads.
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
fasta
:file
FASTA file with draft assembly of ONT data
*.{fasta,fna,fa,fas}
meta2
sam
List of SAM files of short reads mapped against the FASTA input file
*.sam
save_debug
:boolean
Turn debug output on
true|false
*.fasta
FASTA file with polished draft assembly
debug
*.txt
File with debug base information
versions_polypolish
${task.process}
:string
The name of the process
polypolish
The name of the tool
polypolish polish --version |& sed '1!d;s/Polypolish-polish //'
:eval
The expression to obtain the version of the tool
versions
