Calculate pairwise nucleotide identity with respect to a reference sequence
meta
:map
Groovy Map containing information, e.g. [ id:‘test’, single_end:false ]
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
Groovy Map containing information about the reference genome
reference
Fasta of a reference genome. Has to be uncompressed!
compress
:boolean
Set to “true” if fasta output should be compressed
valid_fasta
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*
invalid_fasta
${prefix}_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}
report
*.tsv
Report with some information for every sample, like statistic values. See docs for details
log
*.log
Log file of president
versions_president
${task.process}
:string
The name of the process
president
The name of the tool
president --version |& sed '1!d;s/president v//'
:eval
The expression to obtain the version of the tool
versions
