Identify antimicrobial resistance in gene or protein sequences
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
Nucleotide or protein sequences in FASTA format
*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}
db{:bash}
A compressed tarball of the AMRFinderPlus database to query
*.tar.gz
report{:bash}
${prefix}.tsv{:bash}
AMRFinder+ final report
*.tsv
mutation_report{:bash}
${prefix}-mutations.tsv{:bash}
Report of organism-specific point-mutations
*-mutations.tsv
tool_version{:bash}
VER{:bash}
:string
The version of the tool in string format (useful for downstream tools such as hAMRronization)
db_version{:bash}
DBVER{:bash}
The version of the used database in string format (useful for downstream tools such as hAMRronization)
versions_amrfinderplus{:bash}
${task.process}{:bash}
Process name
amrfinderplus{:bash}
Tool name
amrfinder --version{:bash}
Tool version command
versions_amrfinderplus_database{:bash}
amrfinderplus_database{:bash}
Database name
amrfinder --database amrfinderdb --database_version 2>&1 | grep -oE '[0-9]{4}-[0-9]{2}-[0-9]{2}\.[0-9]+' | tail -1{:bash}
Database version command
versions{:bash}
AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
