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