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}

meta2:map

Groovy Map containing information about the reference genome

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

valid_fasta

meta:file

Fasta file containing sequences which passed the qc (“valid.fasta”). If true is set on the “compress” input value, the file is gz-compressed.

*.{fasta.gz, fasta}

${prefix}_valid.fasta*:file

Fasta file containing sequences which passed the qc (“valid.fasta”). If true is set on the “compress” input value, the file is gz-compressed.

*.{fasta.gz, fasta}

id_fasta:file

Fasta file containing sequences which passed the qc (“valid.fasta”). If true is set on the “compress” input value, the file is gz-compressed.

*.{fasta.gz, fasta}

invalid_fasta

meta:file

Fasta file containing sequences which didn’t pass the qc (“invalid.fasta”). If true is set on the “compress” input value, the files are gz-compressed.

*_invalid.{fasta.gz, fasta}

${prefix}_invalid.fasta*:file

Fasta file containing sequences which didn’t pass the qc (“invalid.fasta”). If true is set on the “compress” input value, the files are gz-compressed.

*_invalid.{fasta.gz, fasta}

id_fasta:file

Fasta file containing sequences which didn’t pass the qc (“invalid.fasta”). If true is set on the “compress” input value, the files are gz-compressed.

*_invalid.{fasta.gz, fasta}

report

meta:file

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

*.tsv

*.tsv:file

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

*.tsv

log

meta:file

Log file of president

*.log

*.log:file

Log file of president

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

president
MIT

Calculate pairwise nucleotide identity with respect to a reference sequence