Description

Calculate pairwise nucleotide identity with respect to a reference sequence

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing information, e.g. [ id:‘test’, single_end

]

fasta (file)

One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed!

*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}

reference (file)

Fasta of a reference genome. Has to be uncompressed!

*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}

compress (boolean)

Set to “true” if fasta output should be compressed

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

fasta (file)

Two fasta files, one with sequences which passed the qc (“valid.fasta”), one with sequences which didn’t pass the qc (“invalid.fasta”). If true is set on the “compress” input value, these files are gz-compressed.

*.{fasta.gz, fasta}

report (file)

Report with some information for every sample, like statistic values. See docs for details

*.tsv

log (file)

Log file of president

*.log

Tools

president
MIT

Calculate pairwise nucleotide identity with respect to a reference sequence