Screen assemblies for antimicrobial resistance against multiple databases
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
assembly{:bash}
:file
FASTA, GenBank or EMBL formatted file
*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}
databasedir{:bash}
:directory
Optional location of local copy of database files, possibly with custom databases set up with abricate --setupdb
abricate --setupdb
*/
report{:bash}
*.txt{:bash}
Tab-delimited report of results
*.{txt}
versions_abricate{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
abricate{:bash}
The tool name
abricate --version | sed 's/^.* //' {:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Mass screening of contigs for antibiotic resistance genes
