Calculate pairwise nucleotide identity with respect to a reference sequence
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!
compress:boolean
Set to “true” if fasta output should be compressed
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
id_fasta:file
invalid_fasta
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
report
Report with some information for every sample, like statistic values. See docs for details
*.tsv
*.tsv:file
log
Log file of president
*.log
*.log:file
versions
versions.yml:file
File containing software versions
versions.yml
