Contiguate draft genome assembly
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
scaffold{:bash}
:file
Fasta file containing scaffold
*.{fasta,fa}
meta2{:bash}
Groovy Map containing genome information e.g. [ id:‘fasta’ ]
fasta{:bash}
FASTA reference file
results{:bash}
${prefix}.*{:bash}
List containing abacas output files [ ‘.abacas.bin’, ‘.abacas.fasta’, ‘.abacas.gaps’, ‘.abacas.gaps.tab’, ‘.abacas.nucmer.delta’, ‘.abacas.nucmer.filtered.delta’, ‘.abacas.nucmer.tiling’, ‘.abacas.tab’, ‘.abacas.unused.contigs.out’, ‘.abacas.MULTIFASTA.fa’ ]
${prefix}.*
versions_abacas{:bash}
${task.process}{:bash}
:string
The name of the process
abacas{:bash}
The name of the tool
abacas.pl --version 2>&1 | grep 'ABACAS\.' | sed 's/ABACAS\.//' || true{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
