Identify antimicrobial resistance in gene or protein sequences
Input
name:type
description
pattern
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}
organism
:string
Organism name as listed by amrfinder --list_organisms
(e.g. ‘Escherichia’). Enables organism-specific point-mutation
screening and the mutation report. Set to ‘’ or [] to disable.
is_proteins
:boolean
Whether the FASTA contains protein sequences (true, passed with -p)
or nucleotide sequences (false, passed with -n)
db
:file
A compressed tarball of the AMRFinderPlus database to query
*.tar.gz
Output
name:type
description
pattern
report
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.tsv
:file
AMRFinder+ final report
*.tsv
mutation_report
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}-mutations.tsv
:file
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
:string
The version of the used database in string format (useful for downstream tools such as hAMRronization)
