Contiguate draft genome assembly
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
scaffold
:file
Fasta file containing scaffold
*.{fasta,fa}
meta2
Groovy Map containing genome information e.g. [ id:‘fasta’ ]
fasta
FASTA reference file
results
${prefix}.*
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’ ]
versions_abacas
${task.process}
:string
The name of the process
abacas
The name of the tool
abacas.pl --version 2>&1 | grep 'ABACAS\.' | sed 's/ABACAS\.//' || true
:eval
The expression to obtain the version of the tool
versions
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.
