Serovar prediction of salmonella assemblies
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
fasta:file
Nucleotide or protein sequences in FASTA format
*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}
tsv
*.tab:file
SISTR serovar prediction
*.{tsv}
allele_fasta
*-allele.fasta:file
FASTA file destination of novel cgMLST alleles
*.{fasta}
allele_json
*-allele.json:file
Allele sequences and info to JSON
*.{json}
cgmlst_csv
*-cgmlst.csv:file
CSV file destination for cgMLST allelic profiles
*.{csv}
versions
versions.yml:file
File containing software versions
versions.yml
Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction
