Description

Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs.

Input

name:type
description
pattern

meta:map

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

fasta:file

A fasta file containing RNA or transcript sequences

*.{fasta,fa}

Output

name:type
description
pattern

rnafold_txt

meta:file

The text Output of RNAfold that

*.{fold}

*.fold:file

The text Output of RNAfold that

*.{fold}

rnafold_ps

meta:file

The text Output of RNAfold that

*.ss

*.ps:file

The text Output of RNAfold that

*.ss

versions

meta:file

File containing software versions

versions.yml

versions.yml:file

File containing software versions

versions.yml

Tools

viennarna
custom

Calculate minimum free energy secondary structures and partition function of RNAs The program reads RNA sequences, calculates their minimum free energy (mfe) structure and prints the mfe structure in bracket notation and its free energy. If not specified differently using commandline arguments, input is accepted from stdin or read from an input file, and output printed to stdout. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.