A tool to reconstruct plasmids in bacterial assemblies
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta
:file
A bacterial genome assembly in FASTA format
*.{fasta,fa,fna}
chromosome
results/chromosome.fasta
FASTA file of all contigs found to belong to the chromosome
chromosome.fasta
contig_report
results/contig_report.txt
Assignment of the contig to chromosome or a particular plasmid grouping
contig_report.txt
plasmids
results/plasmid_*.fasta
Each plasmid group is written to an individual FASTA
plasmid_*.fasta
mobtyper_results
results/mobtyper_results.txt
Aggregate MOB-typer report files for all identified plasmid
mobtyper_results.txt
versions_mobsuite
${task.process}
:string
The name of the process
mobsuite
The name of the tool
mob_recon --version 2>&1 | sed 's/.*mob_recon //; s/ .*//'
:eval
The expression to obtain the version of the tool
versions
Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
