Screen assemblies for antimicrobial resistance against multiple databases
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reports{:bash}
:file
FASTA, GenBank or EMBL formatted file
*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}
report{:bash}
*.txt{:bash}
Tab-delimited report of aggregated results
*.{txt}
versions_abricate_summary{:bash}
${task.process}{:bash}
:string
The name of the process
abricate{:bash}
The name of the tool
abricate --version 2>&1 | sed 's/^.*abricate //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Mass screening of contigs for antibiotic resistance genes
